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cgandini

Hi! the search tool is not working. My apollo-config file is the following:

// default username/password on h2 are given here. see docs for adjusting

dataSource {

    pooled = true

    jmxExport = true

    driverClassName = "org.h2.Driver"

    username = "[hidden email]"

    password = "1789"

}

// environment specific settings

environments {

    development {

        // sample config to turn on debug logging in development e.g. for apollo run-local

        log4j.main = {

            debug "grails.app"

        }

        // sample config to edit apollo specific configs in development mode

        apollo {

            gff3.source = "testing"

        }

        dataSource {

            dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }

    test {

        dataSource {

            dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }


    //note: not necessarily recommended to use h2 in production mode. see precautions

    production {

        dataSource {

            dbCreate = "update"

            //NOTE: production mode uses file instead of mem database

            //Please specify the appropriate file path, otherwise /tmp/prodDb will be used.

            //url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            url = "jdbc:h2:/tmp/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            properties {

               // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation

               jmxEnabled = true

               initialSize = 5

               maxActive = 50

               minIdle = 5

               maxIdle = 25

               maxWait = 10000

               maxAge = 10 * 60000

               timeBetweenEvictionRunsMillis = 5000

               minEvictableIdleTimeMillis = 60000

               validationQuery = "SELECT 1"

               validationQueryTimeout = 3

               validationInterval = 15000

               testOnBorrow = true

               testWhileIdle = true

               testOnReturn = false

               jdbcInterceptors = "ConnectionState"

               defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED

            }

        }

    }



// default apollo settings

apollo {

  default_minimum_intron_size = 1

  history_size = 0

  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"

  track_name_comparator = "/config/track_name_comparator.js"

  use_cds_for_new_transcripts = true

  user_pure_memory_store = true

  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"

  is_partial_translation_allowed = false // unused so far

  get_translation_code = 11

  sequence_search_tools = [

  blat_nuc : [

          search_exe  : "/usr/local/ncbi/blast/bin/blastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast nucleotide",

          params      : ""

  ],

  blat_prot: [

          search_exe  : "/usr/local/ncbi/blast/bin/tblastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast protein to translated nucleotide",

          params      : ""

          //tmp_dir: "/opt/apollo/tmp" optional param

    ]

  ]    

     



  splice_donor_sites = [ "GT" ]

  splice_acceptor_sites = [ "AG"]

  gff3.source= "." bootstrap = false


  info_editor = {

    feature_types = "default"

    attributes = true

    dbxrefs = true

    pubmed_ids = true

    go_ids = true

    comments = true

  }

}


// Uncomment to make changes

//

jbrowse {

    git {

        url= "https://github.com/GMOD/jbrowse"

        tag = "1.12.2-apollo"

////        branch = "master"

        alwaysPull = true

        alwaysRecheck = true

    }

    plugins {

        WebApollo{

            included = true

        }

        NeatHTMLFeatures{

            included = true

        }

        NeatCanvasFeatures{

            included = true

        }

        RegexSequenceSearch{

            included = true

        }

        HideTrackLabels{

            included = true

        }

        MyVariantInfo {

            git = 'https://github.com/GMOD/myvariantviewer'

            branch = 'master'

            alwaysRecheck = "true"

            alwaysPull = "true"

        }

        SashimiPlot {

            git = 'https://github.com/cmdcolin/sashimiplot'

            branch = 'master'

            alwaysPull = "true"

        }

        BlastView {

            git = 'https://github.com/TAMU-CPT/blastview'

            branch = 'master'

            alwaysPull = "true"

        }

        SequenceViews {

            git = 'https://github.com/bhofmei/jbplugin-seqview'

            branch = 'master'

            alwaysPull = "true"

        }

    }

}

}


Which database I have to set as blast database? Do I have to add path to the makeblastdb output of my reference sequence?

Thanks in advance!

Carolina








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Re: Search Tool Configuration

nathandunn

Carolina,

Are you trying to setup blat or blast?  It looks like blast. 

If your binaries are pointing to the correct location then in the organism tab you specify the directory here (we have ours setup for blat):


If you can I would recommend blat, but blast should work as well.

If you run into further errors, please provide the tomcat log (catalina.out) as well.  

Nathan


On Jul 18, 2017, at 6:26 PM, Carolina Gandini <[hidden email]> wrote:


Hi! the search tool is not working. My apollo-config file is the following:

// default username/password on h2 are given here. see docs for adjusting

dataSource {

    pooled = true

    jmxExport = true

    driverClassName = "org.h2.Driver"

    username = "[hidden email]"

    password = "1789"

}

// environment specific settings

environments {

    development {

        // sample config to turn on debug logging in development e.g. for apollo run-local

        log4j.main = {

            debug "grails.app"

        }

        // sample config to edit apollo specific configs in development mode

        apollo {

            gff3.source = "testing"

        }

        dataSource {

            dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }

    test {

        dataSource {

            dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }


    //note: not necessarily recommended to use h2 in production mode. see precautions

    production {

        dataSource {

            dbCreate = "update"

            //NOTE: production mode uses file instead of mem database

            //Please specify the appropriate file path, otherwise /tmp/prodDb will be used.

            //url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            url = "jdbc:h2:/tmp/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            properties {

               // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation

               jmxEnabled = true

               initialSize = 5

               maxActive = 50

               minIdle = 5

               maxIdle = 25

               maxWait = 10000

               maxAge = 10 * 60000

               timeBetweenEvictionRunsMillis = 5000

               minEvictableIdleTimeMillis = 60000

               validationQuery = "SELECT 1"

               validationQueryTimeout = 3

               validationInterval = 15000

               testOnBorrow = true

               testWhileIdle = true

               testOnReturn = false

               jdbcInterceptors = "ConnectionState"

               defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED

            }

        }

    }



// default apollo settings

apollo {

  default_minimum_intron_size = 1

  history_size = 0

  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"

  track_name_comparator = "/config/track_name_comparator.js"

  use_cds_for_new_transcripts = true

  user_pure_memory_store = true

  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"

  is_partial_translation_allowed = false // unused so far

  get_translation_code = 11

  sequence_search_tools = [

  blat_nuc : [

          search_exe  : "/usr/local/ncbi/blast/bin/blastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast nucleotide",

          params      : ""

  ],

  blat_prot: [

          search_exe  : "/usr/local/ncbi/blast/bin/tblastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast protein to translated nucleotide",

          params      : ""

          //tmp_dir: "/opt/apollo/tmp" optional param

    ]

  ]    

     



  splice_donor_sites = [ "GT" ]

  splice_acceptor_sites = [ "AG"]

  gff3.source= "." bootstrap = false


  info_editor = {

    feature_types = "default"

    attributes = true

    dbxrefs = true

    pubmed_ids = true

    go_ids = true

    comments = true

  }

}


// Uncomment to make changes

//

jbrowse {

    git {

        url= "https://github.com/GMOD/jbrowse"

        tag = "1.12.2-apollo"

////        branch = "master"

        alwaysPull = true

        alwaysRecheck = true

    }

    plugins {

        WebApollo{

            included = true

        }

        NeatHTMLFeatures{

            included = true

        }

        NeatCanvasFeatures{

            included = true

        }

        RegexSequenceSearch{

            included = true

        }

        HideTrackLabels{

            included = true

        }

        MyVariantInfo {

            git = 'https://github.com/GMOD/myvariantviewer'

            branch = 'master'

            alwaysRecheck = "true"

            alwaysPull = "true"

        }

        SashimiPlot {

            git = 'https://github.com/cmdcolin/sashimiplot'

            branch = 'master'

            alwaysPull = "true"

        }

        BlastView {

            git = 'https://github.com/TAMU-CPT/blastview'

            branch = 'master'

            alwaysPull = "true"

        }

        SequenceViews {

            git = 'https://github.com/bhofmei/jbplugin-seqview'

            branch = 'master'

            alwaysPull = "true"

        }

    }

}

}


Which database I have to set as blast database? Do I have to add path to the makeblastdb output of my reference sequence?

Thanks in advance!

Carolina






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Re: Search Tool Configuration

cgandini
Hi Nathan,

yes, I have configured for blast. However, I do not understand which database extension I have to specify since the makeblastdb output is composed by 5 files. I wrote in the url the path to the database without extension, as I do with other programs but it did not work.

I am now making a new apollo.war with blat configuration. There is any way to change configuration without making a new .war?

Thanks,

Carolina

On Wed, Jul 19, 2017 at 12:40 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

Are you trying to setup blat or blast?  It looks like blast. 

If your binaries are pointing to the correct location then in the organism tab you specify the directory here (we have ours setup for blat):


If you can I would recommend blat, but blast should work as well.

If you run into further errors, please provide the tomcat log (catalina.out) as well.  

Nathan


On Jul 18, 2017, at 6:26 PM, Carolina Gandini <[hidden email]> wrote:


Hi! the search tool is not working. My apollo-config file is the following:

// default username/password on h2 are given here. see docs for adjusting

dataSource {

    pooled = true

    jmxExport = true

    driverClassName = "org.h2.Driver"

    username = "[hidden email]"

    password = "1789"

}

// environment specific settings

environments {

    development {

        // sample config to turn on debug logging in development e.g. for apollo run-local

        log4j.main = {

            debug "grails.app"

        }

        // sample config to edit apollo specific configs in development mode

        apollo {

            gff3.source = "testing"

        }

        dataSource {

            dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }

    test {

        dataSource {

            dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }


    //note: not necessarily recommended to use h2 in production mode. see precautions

    production {

        dataSource {

            dbCreate = "update"

            //NOTE: production mode uses file instead of mem database

            //Please specify the appropriate file path, otherwise /tmp/prodDb will be used.

            //url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            url = "jdbc:h2:/tmp/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            properties {

               // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation

               jmxEnabled = true

               initialSize = 5

               maxActive = 50

               minIdle = 5

               maxIdle = 25

               maxWait = 10000

               maxAge = 10 * 60000

               timeBetweenEvictionRunsMillis = 5000

               minEvictableIdleTimeMillis = 60000

               validationQuery = "SELECT 1"

               validationQueryTimeout = 3

               validationInterval = 15000

               testOnBorrow = true

               testWhileIdle = true

               testOnReturn = false

               jdbcInterceptors = "ConnectionState"

               defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED

            }

        }

    }



// default apollo settings

apollo {

  default_minimum_intron_size = 1

  history_size = 0

  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"

  track_name_comparator = "/config/track_name_comparator.js"

  use_cds_for_new_transcripts = true

  user_pure_memory_store = true

  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"

  is_partial_translation_allowed = false // unused so far

  get_translation_code = 11

  sequence_search_tools = [

  blat_nuc : [

          search_exe  : "/usr/local/ncbi/blast/bin/blastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast nucleotide",

          params      : ""

  ],

  blat_prot: [

          search_exe  : "/usr/local/ncbi/blast/bin/tblastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast protein to translated nucleotide",

          params      : ""

          //tmp_dir: "/opt/apollo/tmp" optional param

    ]

  ]    

     



  splice_donor_sites = [ "GT" ]

  splice_acceptor_sites = [ "AG"]

  gff3.source= "." bootstrap = false


  info_editor = {

    feature_types = "default"

    attributes = true

    dbxrefs = true

    pubmed_ids = true

    go_ids = true

    comments = true

  }

}


// Uncomment to make changes

//

jbrowse {

    git {

        url= "https://github.com/GMOD/jbrowse"

        tag = "1.12.2-apollo"

////        branch = "master"

        alwaysPull = true

        alwaysRecheck = true

    }

    plugins {

        WebApollo{

            included = true

        }

        NeatHTMLFeatures{

            included = true

        }

        NeatCanvasFeatures{

            included = true

        }

        RegexSequenceSearch{

            included = true

        }

        HideTrackLabels{

            included = true

        }

        MyVariantInfo {

            git = 'https://github.com/GMOD/myvariantviewer'

            branch = 'master'

            alwaysRecheck = "true"

            alwaysPull = "true"

        }

        SashimiPlot {

            git = 'https://github.com/cmdcolin/sashimiplot'

            branch = 'master'

            alwaysPull = "true"

        }

        BlastView {

            git = 'https://github.com/TAMU-CPT/blastview'

            branch = 'master'

            alwaysPull = "true"

        }

        SequenceViews {

            git = 'https://github.com/bhofmei/jbplugin-seqview'

            branch = 'master'

            alwaysPull = "true"

        }

    }

}

}


Which database I have to set as blast database? Do I have to add path to the makeblastdb output of my reference sequence?

Thanks in advance!

Carolina






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Search Tool Configuration

nathandunn

Carolina,

It just runs a blast from the command-line from within the server.  

e.g., 

blastn -db <what you put in the organism directory>  -query <fasta you provided> -out <output arg> -outfmt 6

If blat meets your needs, I would recommend that, as its much quicker.  

If you change your config you’ll have to run “./apollo deploy” again and update the server.  Here are the instructions I use when I make changes to a production config:

  • Create a new war file as below: ./apollo deploy.
  • Turn off tomcat and remove the old apollo directory and .war file in the webapps folder.
  • Copy in new .war file with the same name.
  • Restart tomcat and you are ready to go.


Nathan


On Jul 20, 2017, at 5:24 AM, Carolina Gandini <[hidden email]> wrote:

Hi Nathan,

yes, I have configured for blast. However, I do not understand which database extension I have to specify since the makeblastdb output is composed by 5 files. I wrote in the url the path to the database without extension, as I do with other programs but it did not work.

I am now making a new apollo.war with blat configuration. There is any way to change configuration without making a new .war?

Thanks,

Carolina

On Wed, Jul 19, 2017 at 12:40 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

Are you trying to setup blat or blast?  It looks like blast. 

If your binaries are pointing to the correct location then in the organism tab you specify the directory here (we have ours setup for blat):

<Screen Shot 2017-07-19 at 8.38.08 AM.png>

If you can I would recommend blat, but blast should work as well.

If you run into further errors, please provide the tomcat log (catalina.out) as well.  

Nathan


On Jul 18, 2017, at 6:26 PM, Carolina Gandini <[hidden email]> wrote:


Hi! the search tool is not working. My apollo-config file is the following:

// default username/password on h2 are given here. see docs for adjusting

dataSource {

    pooled = true

    jmxExport = true

    driverClassName = "org.h2.Driver"

    username = "[hidden email]"

    password = "1789"

}

// environment specific settings

environments {

    development {

        // sample config to turn on debug logging in development e.g. for apollo run-local

        log4j.main = {

            debug "grails.app"

        }

        // sample config to edit apollo specific configs in development mode

        apollo {

            gff3.source = "testing"

        }

        dataSource {

            dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }

    test {

        dataSource {

            dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }


    //note: not necessarily recommended to use h2 in production mode. see precautions

    production {

        dataSource {

            dbCreate = "update"

            //NOTE: production mode uses file instead of mem database

            //Please specify the appropriate file path, otherwise /tmp/prodDb will be used.

            //url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            url = "jdbc:h2:/tmp/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            properties {

               // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation

               jmxEnabled = true

               initialSize = 5

               maxActive = 50

               minIdle = 5

               maxIdle = 25

               maxWait = 10000

               maxAge = 10 * 60000

               timeBetweenEvictionRunsMillis = 5000

               minEvictableIdleTimeMillis = 60000

               validationQuery = "SELECT 1"

               validationQueryTimeout = 3

               validationInterval = 15000

               testOnBorrow = true

               testWhileIdle = true

               testOnReturn = false

               jdbcInterceptors = "ConnectionState"

               defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED

            }

        }

    }



// default apollo settings

apollo {

  default_minimum_intron_size = 1

  history_size = 0

  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"

  track_name_comparator = "/config/track_name_comparator.js"

  use_cds_for_new_transcripts = true

  user_pure_memory_store = true

  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"

  is_partial_translation_allowed = false // unused so far

  get_translation_code = 11

  sequence_search_tools = [

  blat_nuc : [

          search_exe  : "/usr/local/ncbi/blast/bin/blastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast nucleotide",

          params      : ""

  ],

  blat_prot: [

          search_exe  : "/usr/local/ncbi/blast/bin/tblastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast protein to translated nucleotide",

          params      : ""

          //tmp_dir: "/opt/apollo/tmp" optional param

    ]

  ]    

     



  splice_donor_sites = [ "GT" ]

  splice_acceptor_sites = [ "AG"]

  gff3.source= "." bootstrap = false


  info_editor = {

    feature_types = "default"

    attributes = true

    dbxrefs = true

    pubmed_ids = true

    go_ids = true

    comments = true

  }

}


// Uncomment to make changes

//

jbrowse {

    git {

        url= "https://github.com/GMOD/jbrowse"

        tag = "1.12.2-apollo"

////        branch = "master"

        alwaysPull = true

        alwaysRecheck = true

    }

    plugins {

        WebApollo{

            included = true

        }

        NeatHTMLFeatures{

            included = true

        }

        NeatCanvasFeatures{

            included = true

        }

        RegexSequenceSearch{

            included = true

        }

        HideTrackLabels{

            included = true

        }

        MyVariantInfo {

            git = 'https://github.com/GMOD/myvariantviewer'

            branch = 'master'

            alwaysRecheck = "true"

            alwaysPull = "true"

        }

        SashimiPlot {

            git = 'https://github.com/cmdcolin/sashimiplot'

            branch = 'master'

            alwaysPull = "true"

        }

        BlastView {

            git = 'https://github.com/TAMU-CPT/blastview'

            branch = 'master'

            alwaysPull = "true"

        }

        SequenceViews {

            git = 'https://github.com/bhofmei/jbplugin-seqview'

            branch = 'master'

            alwaysPull = "true"

        }

    }

}

}


Which database I have to set as blast database? Do I have to add path to the makeblastdb output of my reference sequence?

Thanks in advance!

Carolina






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Re: Search Tool Configuration

cgandini
Nathan,

I did that, now is working. So a new question arise :). I do not understand how to annotate a highlated region (blat result).

Thanks,

Carolina

On Thu, Jul 20, 2017 at 12:39 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

It just runs a blast from the command-line from within the server.  

e.g., 

blastn -db <what you put in the organism directory>  -query <fasta you provided> -out <output arg> -outfmt 6

If blat meets your needs, I would recommend that, as its much quicker.  

If you change your config you’ll have to run “./apollo deploy” again and update the server.  Here are the instructions I use when I make changes to a production config:

  • Create a new war file as below: ./apollo deploy.
  • Turn off tomcat and remove the old apollo directory and .war file in the webapps folder.
  • Copy in new .war file with the same name.
  • Restart tomcat and you are ready to go.


Nathan


On Jul 20, 2017, at 5:24 AM, Carolina Gandini <[hidden email]> wrote:

Hi Nathan,

yes, I have configured for blast. However, I do not understand which database extension I have to specify since the makeblastdb output is composed by 5 files. I wrote in the url the path to the database without extension, as I do with other programs but it did not work.

I am now making a new apollo.war with blat configuration. There is any way to change configuration without making a new .war?

Thanks,

Carolina

On Wed, Jul 19, 2017 at 12:40 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

Are you trying to setup blat or blast?  It looks like blast. 

If your binaries are pointing to the correct location then in the organism tab you specify the directory here (we have ours setup for blat):

<Screen Shot 2017-07-19 at 8.38.08 AM.png>

If you can I would recommend blat, but blast should work as well.

If you run into further errors, please provide the tomcat log (catalina.out) as well.  

Nathan


On Jul 18, 2017, at 6:26 PM, Carolina Gandini <[hidden email]> wrote:


Hi! the search tool is not working. My apollo-config file is the following:

// default username/password on h2 are given here. see docs for adjusting

dataSource {

    pooled = true

    jmxExport = true

    driverClassName = "org.h2.Driver"

    username = "[hidden email]"

    password = "1789"

}

// environment specific settings

environments {

    development {

        // sample config to turn on debug logging in development e.g. for apollo run-local

        log4j.main = {

            debug "grails.app"

        }

        // sample config to edit apollo specific configs in development mode

        apollo {

            gff3.source = "testing"

        }

        dataSource {

            dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }

    test {

        dataSource {

            dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }


    //note: not necessarily recommended to use h2 in production mode. see precautions

    production {

        dataSource {

            dbCreate = "update"

            //NOTE: production mode uses file instead of mem database

            //Please specify the appropriate file path, otherwise /tmp/prodDb will be used.

            //url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            url = "jdbc:h2:/tmp/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            properties {

               // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation

               jmxEnabled = true

               initialSize = 5

               maxActive = 50

               minIdle = 5

               maxIdle = 25

               maxWait = 10000

               maxAge = 10 * 60000

               timeBetweenEvictionRunsMillis = 5000

               minEvictableIdleTimeMillis = 60000

               validationQuery = "SELECT 1"

               validationQueryTimeout = 3

               validationInterval = 15000

               testOnBorrow = true

               testWhileIdle = true

               testOnReturn = false

               jdbcInterceptors = "ConnectionState"

               defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED

            }

        }

    }



// default apollo settings

apollo {

  default_minimum_intron_size = 1

  history_size = 0

  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"

  track_name_comparator = "/config/track_name_comparator.js"

  use_cds_for_new_transcripts = true

  user_pure_memory_store = true

  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"

  is_partial_translation_allowed = false // unused so far

  get_translation_code = 11

  sequence_search_tools = [

  blat_nuc : [

          search_exe  : "/usr/local/ncbi/blast/bin/blastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast nucleotide",

          params      : ""

  ],

  blat_prot: [

          search_exe  : "/usr/local/ncbi/blast/bin/tblastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast protein to translated nucleotide",

          params      : ""

          //tmp_dir: "/opt/apollo/tmp" optional param

    ]

  ]    

     



  splice_donor_sites = [ "GT" ]

  splice_acceptor_sites = [ "AG"]

  gff3.source= "." bootstrap = false


  info_editor = {

    feature_types = "default"

    attributes = true

    dbxrefs = true

    pubmed_ids = true

    go_ids = true

    comments = true

  }

}


// Uncomment to make changes

//

jbrowse {

    git {

        url= "https://github.com/GMOD/jbrowse"

        tag = "1.12.2-apollo"

////        branch = "master"

        alwaysPull = true

        alwaysRecheck = true

    }

    plugins {

        WebApollo{

            included = true

        }

        NeatHTMLFeatures{

            included = true

        }

        NeatCanvasFeatures{

            included = true

        }

        RegexSequenceSearch{

            included = true

        }

        HideTrackLabels{

            included = true

        }

        MyVariantInfo {

            git = 'https://github.com/GMOD/myvariantviewer'

            branch = 'master'

            alwaysRecheck = "true"

            alwaysPull = "true"

        }

        SashimiPlot {

            git = 'https://github.com/cmdcolin/sashimiplot'

            branch = 'master'

            alwaysPull = "true"

        }

        BlastView {

            git = 'https://github.com/TAMU-CPT/blastview'

            branch = 'master'

            alwaysPull = "true"

        }

        SequenceViews {

            git = 'https://github.com/bhofmei/jbplugin-seqview'

            branch = 'master'

            alwaysPull = "true"

        }

    }

}

}


Which database I have to set as blast database? Do I have to add path to the makeblastdb output of my reference sequence?

Thanks in advance!

Carolina






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.


Screen Shot 2017-07-20 at 1.24.11 PM.png (394K) Download Attachment
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Re: Search Tool Configuration

nathandunn

I believe the idea is that blat supports your annotation.   See the user’s guide under the Annotation heading for more detail:  http://genomearchitect.org/users-guide/

There are users who create Tracks out of BLAST / BLAT results (e.g,. https://github.com/NAL-i5K/genomics-workspace) for annotation, but I don’t know if that would be overkill  for what you want.   The setup is significantly more involved. 

Nathan



On Jul 20, 2017, at 9:24 AM, Carolina Gandini <[hidden email]> wrote:

Nathan,

I did that, now is working. So a new question arise :). I do not understand how to annotate a highlated region (blat result).

Thanks,

Carolina

On Thu, Jul 20, 2017 at 12:39 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

It just runs a blast from the command-line from within the server.  

e.g., 

blastn -db <what you put in the organism directory>  -query <fasta you provided> -out <output arg> -outfmt 6

If blat meets your needs, I would recommend that, as its much quicker.  

If you change your config you’ll have to run “./apollo deploy” again and update the server.  Here are the instructions I use when I make changes to a production config:

  • Create a new war file as below: ./apollo deploy.
  • Turn off tomcat and remove the old apollo directory and .war file in the webapps folder.
  • Copy in new .war file with the same name.
  • Restart tomcat and you are ready to go.


Nathan


On Jul 20, 2017, at 5:24 AM, Carolina Gandini <[hidden email]> wrote:

Hi Nathan,

yes, I have configured for blast. However, I do not understand which database extension I have to specify since the makeblastdb output is composed by 5 files. I wrote in the url the path to the database without extension, as I do with other programs but it did not work.

I am now making a new apollo.war with blat configuration. There is any way to change configuration without making a new .war?

Thanks,

Carolina

On Wed, Jul 19, 2017 at 12:40 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

Are you trying to setup blat or blast?  It looks like blast. 

If your binaries are pointing to the correct location then in the organism tab you specify the directory here (we have ours setup for blat):

<Screen Shot 2017-07-19 at 8.38.08 AM.png>

If you can I would recommend blat, but blast should work as well.

If you run into further errors, please provide the tomcat log (catalina.out) as well.  

Nathan


On Jul 18, 2017, at 6:26 PM, Carolina Gandini <[hidden email]> wrote:


Hi! the search tool is not working. My apollo-config file is the following:

// default username/password on h2 are given here. see docs for adjusting

dataSource {

    pooled = true

    jmxExport = true

    driverClassName = "org.h2.Driver"

    username = "[hidden email]"

    password = "1789"

}

// environment specific settings

environments {

    development {

        // sample config to turn on debug logging in development e.g. for apollo run-local

        log4j.main = {

            debug "grails.app"

        }

        // sample config to edit apollo specific configs in development mode

        apollo {

            gff3.source = "testing"

        }

        dataSource {

            dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }

    test {

        dataSource {

            dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }


    //note: not necessarily recommended to use h2 in production mode. see precautions

    production {

        dataSource {

            dbCreate = "update"

            //NOTE: production mode uses file instead of mem database

            //Please specify the appropriate file path, otherwise /tmp/prodDb will be used.

            //url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            url = "jdbc:h2:/tmp/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            properties {

               // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation

               jmxEnabled = true

               initialSize = 5

               maxActive = 50

               minIdle = 5

               maxIdle = 25

               maxWait = 10000

               maxAge = 10 * 60000

               timeBetweenEvictionRunsMillis = 5000

               minEvictableIdleTimeMillis = 60000

               validationQuery = "SELECT 1"

               validationQueryTimeout = 3

               validationInterval = 15000

               testOnBorrow = true

               testWhileIdle = true

               testOnReturn = false

               jdbcInterceptors = "ConnectionState"

               defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED

            }

        }

    }



// default apollo settings

apollo {

  default_minimum_intron_size = 1

  history_size = 0

  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"

  track_name_comparator = "/config/track_name_comparator.js"

  use_cds_for_new_transcripts = true

  user_pure_memory_store = true

  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"

  is_partial_translation_allowed = false // unused so far

  get_translation_code = 11

  sequence_search_tools = [

  blat_nuc : [

          search_exe  : "/usr/local/ncbi/blast/bin/blastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast nucleotide",

          params      : ""

  ],

  blat_prot: [

          search_exe  : "/usr/local/ncbi/blast/bin/tblastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast protein to translated nucleotide",

          params      : ""

          //tmp_dir: "/opt/apollo/tmp" optional param

    ]

  ]    

     



  splice_donor_sites = [ "GT" ]

  splice_acceptor_sites = [ "AG"]

  gff3.source= "." bootstrap = false


  info_editor = {

    feature_types = "default"

    attributes = true

    dbxrefs = true

    pubmed_ids = true

    go_ids = true

    comments = true

  }

}


// Uncomment to make changes

//

jbrowse {

    git {

        url= "https://github.com/GMOD/jbrowse"

        tag = "1.12.2-apollo"

////        branch = "master"

        alwaysPull = true

        alwaysRecheck = true

    }

    plugins {

        WebApollo{

            included = true

        }

        NeatHTMLFeatures{

            included = true

        }

        NeatCanvasFeatures{

            included = true

        }

        RegexSequenceSearch{

            included = true

        }

        HideTrackLabels{

            included = true

        }

        MyVariantInfo {

            git = 'https://github.com/GMOD/myvariantviewer'

            branch = 'master'

            alwaysRecheck = "true"

            alwaysPull = "true"

        }

        SashimiPlot {

            git = 'https://github.com/cmdcolin/sashimiplot'

            branch = 'master'

            alwaysPull = "true"

        }

        BlastView {

            git = 'https://github.com/TAMU-CPT/blastview'

            branch = 'master'

            alwaysPull = "true"

        }

        SequenceViews {

            git = 'https://github.com/bhofmei/jbplugin-seqview'

            branch = 'master'

            alwaysPull = "true"

        }

    }

}

}


Which database I have to set as blast database? Do I have to add path to the makeblastdb output of my reference sequence?

Thanks in advance!

Carolina






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<Screen Shot 2017-07-20 at 1.24.11 PM.png>


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Re: Search Tool Configuration

Monica Munoz-Torres
In reply to this post by cgandini
Dear Carolina, all,

The search tool assists you in finding regions with significant sequence similarity to a string of interest (amino acid or nucleotide). Once the region has been identified, you should display all available evidence in support of gene models (or other elements of the genome) that have been predicted / identified in the region. For instance, you could select drag any overlapping gene models within the 'yellow' highlight and use this model to begin your annotation. 

You can see an example that shows how to use the results of a blat search to conduct an annotation in this instructional video, available at http://bit.ly/apollo-video-2, and from minutes 47 through 59 (approx.). Please keep in mind this video was addressed to a community that has customized certain aspects around community curation using - so it may contain a few technical details that will not apply to your case. (Note: Unfortunately, the video has not yet been captioned, so please accept my apologies if this is a limitation for you or anyone in your team. If so, I can work on providing a transcript of that section).

As Nathan mentioned, you may also read a little more on the functionality of the search tool using blat by visiting our User Guide (http://genomearchitect.org/users-guide/) and reading the section on how to "Search for a specific sequence."

We hope this is useful, but please do not hesitate to send word with further questions about Apollo configuration, installation, and use. We will be delighted to assist you in any way we may. 

cheers, 
~moni.



On Thu, Jul 20, 2017 at 9:24 AM, Carolina Gandini <[hidden email]> wrote:
Nathan,

I did that, now is working. So a new question arise :). I do not understand how to annotate a highlated region (blat result).

Thanks,

Carolina

On Thu, Jul 20, 2017 at 12:39 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

It just runs a blast from the command-line from within the server.  

e.g., 

blastn -db <what you put in the organism directory>  -query <fasta you provided> -out <output arg> -outfmt 6

If blat meets your needs, I would recommend that, as its much quicker.  

If you change your config you’ll have to run “./apollo deploy” again and update the server.  Here are the instructions I use when I make changes to a production config:

  • Create a new war file as below: ./apollo deploy.
  • Turn off tomcat and remove the old apollo directory and .war file in the webapps folder.
  • Copy in new .war file with the same name.
  • Restart tomcat and you are ready to go.


Nathan


On Jul 20, 2017, at 5:24 AM, Carolina Gandini <[hidden email]> wrote:

Hi Nathan,

yes, I have configured for blast. However, I do not understand which database extension I have to specify since the makeblastdb output is composed by 5 files. I wrote in the url the path to the database without extension, as I do with other programs but it did not work.

I am now making a new apollo.war with blat configuration. There is any way to change configuration without making a new .war?

Thanks,

Carolina

On Wed, Jul 19, 2017 at 12:40 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

Are you trying to setup blat or blast?  It looks like blast. 

If your binaries are pointing to the correct location then in the organism tab you specify the directory here (we have ours setup for blat):

<Screen Shot 2017-07-19 at 8.38.08 AM.png>

If you can I would recommend blat, but blast should work as well.

If you run into further errors, please provide the tomcat log (catalina.out) as well.  

Nathan


On Jul 18, 2017, at 6:26 PM, Carolina Gandini <[hidden email]> wrote:


Hi! the search tool is not working. My apollo-config file is the following:

// default username/password on h2 are given here. see docs for adjusting

dataSource {

    pooled = true

    jmxExport = true

    driverClassName = "org.h2.Driver"

    username = "[hidden email]"

    password = "1789"

}

// environment specific settings

environments {

    development {

        // sample config to turn on debug logging in development e.g. for apollo run-local

        log4j.main = {

            debug "grails.app"

        }

        // sample config to edit apollo specific configs in development mode

        apollo {

            gff3.source = "testing"

        }

        dataSource {

            dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }

    test {

        dataSource {

            dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }


    //note: not necessarily recommended to use h2 in production mode. see precautions

    production {

        dataSource {

            dbCreate = "update"

            //NOTE: production mode uses file instead of mem database

            //Please specify the appropriate file path, otherwise /tmp/prodDb will be used.

            //url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            url = "jdbc:h2:/tmp/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            properties {

               // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation

               jmxEnabled = true

               initialSize = 5

               maxActive = 50

               minIdle = 5

               maxIdle = 25

               maxWait = 10000

               maxAge = 10 * 60000

               timeBetweenEvictionRunsMillis = 5000

               minEvictableIdleTimeMillis = 60000

               validationQuery = "SELECT 1"

               validationQueryTimeout = 3

               validationInterval = 15000

               testOnBorrow = true

               testWhileIdle = true

               testOnReturn = false

               jdbcInterceptors = "ConnectionState"

               defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED

            }

        }

    }



// default apollo settings

apollo {

  default_minimum_intron_size = 1

  history_size = 0

  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"

  track_name_comparator = "/config/track_name_comparator.js"

  use_cds_for_new_transcripts = true

  user_pure_memory_store = true

  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"

  is_partial_translation_allowed = false // unused so far

  get_translation_code = 11

  sequence_search_tools = [

  blat_nuc : [

          search_exe  : "/usr/local/ncbi/blast/bin/blastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast nucleotide",

          params      : ""

  ],

  blat_prot: [

          search_exe  : "/usr/local/ncbi/blast/bin/tblastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast protein to translated nucleotide",

          params      : ""

          //tmp_dir: "/opt/apollo/tmp" optional param

    ]

  ]    

     



  splice_donor_sites = [ "GT" ]

  splice_acceptor_sites = [ "AG"]

  gff3.source= "." bootstrap = false


  info_editor = {

    feature_types = "default"

    attributes = true

    dbxrefs = true

    pubmed_ids = true

    go_ids = true

    comments = true

  }

}


// Uncomment to make changes

//

jbrowse {

    git {

        url= "https://github.com/GMOD/jbrowse"

        tag = "1.12.2-apollo"

////        branch = "master"

        alwaysPull = true

        alwaysRecheck = true

    }

    plugins {

        WebApollo{

            included = true

        }

        NeatHTMLFeatures{

            included = true

        }

        NeatCanvasFeatures{

            included = true

        }

        RegexSequenceSearch{

            included = true

        }

        HideTrackLabels{

            included = true

        }

        MyVariantInfo {

            git = 'https://github.com/GMOD/myvariantviewer'

            branch = 'master'

            alwaysRecheck = "true"

            alwaysPull = "true"

        }

        SashimiPlot {

            git = 'https://github.com/cmdcolin/sashimiplot'

            branch = 'master'

            alwaysPull = "true"

        }

        BlastView {

            git = 'https://github.com/TAMU-CPT/blastview'

            branch = 'master'

            alwaysPull = "true"

        }

        SequenceViews {

            git = 'https://github.com/bhofmei/jbplugin-seqview'

            branch = 'master'

            alwaysPull = "true"

        }

    }

}

}


Which database I have to set as blast database? Do I have to add path to the makeblastdb output of my reference sequence?

Thanks in advance!

Carolina






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--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




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Re: Search Tool Configuration

cgandini
Monica,

I was hoping to use the tool in a different manner. It would be nice if you can select the blasted region and just annotate it. In my case I am annotating a genome in which genes are extremely conserved, so there is no need to predict genes and corroborate them, you just need a 100% cover between the query CDS and your gene. 

I think the tool is not the one I was looking for.

Thanks for all, regards!

Carolina


On Thu, Jul 20, 2017 at 4:49 PM, Monica Munoz-Torres <[hidden email]> wrote:
Dear Carolina, all,

The search tool assists you in finding regions with significant sequence similarity to a string of interest (amino acid or nucleotide). Once the region has been identified, you should display all available evidence in support of gene models (or other elements of the genome) that have been predicted / identified in the region. For instance, you could select drag any overlapping gene models within the 'yellow' highlight and use this model to begin your annotation. 

You can see an example that shows how to use the results of a blat search to conduct an annotation in this instructional video, available at http://bit.ly/apollo-video-2, and from minutes 47 through 59 (approx.). Please keep in mind this video was addressed to a community that has customized certain aspects around community curation using - so it may contain a few technical details that will not apply to your case. (Note: Unfortunately, the video has not yet been captioned, so please accept my apologies if this is a limitation for you or anyone in your team. If so, I can work on providing a transcript of that section).

As Nathan mentioned, you may also read a little more on the functionality of the search tool using blat by visiting our User Guide (http://genomearchitect.org/users-guide/) and reading the section on how to "Search for a specific sequence."

We hope this is useful, but please do not hesitate to send word with further questions about Apollo configuration, installation, and use. We will be delighted to assist you in any way we may. 

cheers, 
~moni.



On Thu, Jul 20, 2017 at 9:24 AM, Carolina Gandini <[hidden email]> wrote:
Nathan,

I did that, now is working. So a new question arise :). I do not understand how to annotate a highlated region (blat result).

Thanks,

Carolina

On Thu, Jul 20, 2017 at 12:39 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

It just runs a blast from the command-line from within the server.  

e.g., 

blastn -db <what you put in the organism directory>  -query <fasta you provided> -out <output arg> -outfmt 6

If blat meets your needs, I would recommend that, as its much quicker.  

If you change your config you’ll have to run “./apollo deploy” again and update the server.  Here are the instructions I use when I make changes to a production config:

  • Create a new war file as below: ./apollo deploy.
  • Turn off tomcat and remove the old apollo directory and .war file in the webapps folder.
  • Copy in new .war file with the same name.
  • Restart tomcat and you are ready to go.


Nathan


On Jul 20, 2017, at 5:24 AM, Carolina Gandini <[hidden email]> wrote:

Hi Nathan,

yes, I have configured for blast. However, I do not understand which database extension I have to specify since the makeblastdb output is composed by 5 files. I wrote in the url the path to the database without extension, as I do with other programs but it did not work.

I am now making a new apollo.war with blat configuration. There is any way to change configuration without making a new .war?

Thanks,

Carolina

On Wed, Jul 19, 2017 at 12:40 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

Are you trying to setup blat or blast?  It looks like blast. 

If your binaries are pointing to the correct location then in the organism tab you specify the directory here (we have ours setup for blat):

<Screen Shot 2017-07-19 at 8.38.08 AM.png>

If you can I would recommend blat, but blast should work as well.

If you run into further errors, please provide the tomcat log (catalina.out) as well.  

Nathan


On Jul 18, 2017, at 6:26 PM, Carolina Gandini <[hidden email]> wrote:


Hi! the search tool is not working. My apollo-config file is the following:

// default username/password on h2 are given here. see docs for adjusting

dataSource {

    pooled = true

    jmxExport = true

    driverClassName = "org.h2.Driver"

    username = "[hidden email]"

    password = "1789"

}

// environment specific settings

environments {

    development {

        // sample config to turn on debug logging in development e.g. for apollo run-local

        log4j.main = {

            debug "grails.app"

        }

        // sample config to edit apollo specific configs in development mode

        apollo {

            gff3.source = "testing"

        }

        dataSource {

            dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }

    test {

        dataSource {

            dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }


    //note: not necessarily recommended to use h2 in production mode. see precautions

    production {

        dataSource {

            dbCreate = "update"

            //NOTE: production mode uses file instead of mem database

            //Please specify the appropriate file path, otherwise /tmp/prodDb will be used.

            //url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            url = "jdbc:h2:/tmp/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            properties {

               // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation

               jmxEnabled = true

               initialSize = 5

               maxActive = 50

               minIdle = 5

               maxIdle = 25

               maxWait = 10000

               maxAge = 10 * 60000

               timeBetweenEvictionRunsMillis = 5000

               minEvictableIdleTimeMillis = 60000

               validationQuery = "SELECT 1"

               validationQueryTimeout = 3

               validationInterval = 15000

               testOnBorrow = true

               testWhileIdle = true

               testOnReturn = false

               jdbcInterceptors = "ConnectionState"

               defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED

            }

        }

    }



// default apollo settings

apollo {

  default_minimum_intron_size = 1

  history_size = 0

  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"

  track_name_comparator = "/config/track_name_comparator.js"

  use_cds_for_new_transcripts = true

  user_pure_memory_store = true

  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"

  is_partial_translation_allowed = false // unused so far

  get_translation_code = 11

  sequence_search_tools = [

  blat_nuc : [

          search_exe  : "/usr/local/ncbi/blast/bin/blastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast nucleotide",

          params      : ""

  ],

  blat_prot: [

          search_exe  : "/usr/local/ncbi/blast/bin/tblastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast protein to translated nucleotide",

          params      : ""

          //tmp_dir: "/opt/apollo/tmp" optional param

    ]

  ]    

     



  splice_donor_sites = [ "GT" ]

  splice_acceptor_sites = [ "AG"]

  gff3.source= "." bootstrap = false


  info_editor = {

    feature_types = "default"

    attributes = true

    dbxrefs = true

    pubmed_ids = true

    go_ids = true

    comments = true

  }

}


// Uncomment to make changes

//

jbrowse {

    git {

        url= "https://github.com/GMOD/jbrowse"

        tag = "1.12.2-apollo"

////        branch = "master"

        alwaysPull = true

        alwaysRecheck = true

    }

    plugins {

        WebApollo{

            included = true

        }

        NeatHTMLFeatures{

            included = true

        }

        NeatCanvasFeatures{

            included = true

        }

        RegexSequenceSearch{

            included = true

        }

        HideTrackLabels{

            included = true

        }

        MyVariantInfo {

            git = 'https://github.com/GMOD/myvariantviewer'

            branch = 'master'

            alwaysRecheck = "true"

            alwaysPull = "true"

        }

        SashimiPlot {

            git = 'https://github.com/cmdcolin/sashimiplot'

            branch = 'master'

            alwaysPull = "true"

        }

        BlastView {

            git = 'https://github.com/TAMU-CPT/blastview'

            branch = 'master'

            alwaysPull = "true"

        }

        SequenceViews {

            git = 'https://github.com/bhofmei/jbplugin-seqview'

            branch = 'master'

            alwaysPull = "true"

        }

    }

}

}


Which database I have to set as blast database? Do I have to add path to the makeblastdb output of my reference sequence?

Thanks in advance!

Carolina






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Search Tool Configuration

Monica Munoz-Torres
Hi Carolina, 

Thanks for responding. 

Unfortunately, I am having difficulty understanding your workflow for this. That's my fault. I'll send you a private message with a few questions to see if I can understand better and perhaps be more helpful. 

cheers, 
~moni.  

On Tue, Jul 25, 2017 at 6:33 AM, Carolina Gandini <[hidden email]> wrote:
Monica,

I was hoping to use the tool in a different manner. It would be nice if you can select the blasted region and just annotate it. In my case I am annotating a genome in which genes are extremely conserved, so there is no need to predict genes and corroborate them, you just need a 100% cover between the query CDS and your gene. 

I think the tool is not the one I was looking for.

Thanks for all, regards!

Carolina


On Thu, Jul 20, 2017 at 4:49 PM, Monica Munoz-Torres <[hidden email]> wrote:
Dear Carolina, all,

The search tool assists you in finding regions with significant sequence similarity to a string of interest (amino acid or nucleotide). Once the region has been identified, you should display all available evidence in support of gene models (or other elements of the genome) that have been predicted / identified in the region. For instance, you could select drag any overlapping gene models within the 'yellow' highlight and use this model to begin your annotation. 

You can see an example that shows how to use the results of a blat search to conduct an annotation in this instructional video, available at http://bit.ly/apollo-video-2, and from minutes 47 through 59 (approx.). Please keep in mind this video was addressed to a community that has customized certain aspects around community curation using - so it may contain a few technical details that will not apply to your case. (Note: Unfortunately, the video has not yet been captioned, so please accept my apologies if this is a limitation for you or anyone in your team. If so, I can work on providing a transcript of that section).

As Nathan mentioned, you may also read a little more on the functionality of the search tool using blat by visiting our User Guide (http://genomearchitect.org/users-guide/) and reading the section on how to "Search for a specific sequence."

We hope this is useful, but please do not hesitate to send word with further questions about Apollo configuration, installation, and use. We will be delighted to assist you in any way we may. 

cheers, 
~moni.



On Thu, Jul 20, 2017 at 9:24 AM, Carolina Gandini <[hidden email]> wrote:
Nathan,

I did that, now is working. So a new question arise :). I do not understand how to annotate a highlated region (blat result).

Thanks,

Carolina

On Thu, Jul 20, 2017 at 12:39 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

It just runs a blast from the command-line from within the server.  

e.g., 

blastn -db <what you put in the organism directory>  -query <fasta you provided> -out <output arg> -outfmt 6

If blat meets your needs, I would recommend that, as its much quicker.  

If you change your config you’ll have to run “./apollo deploy” again and update the server.  Here are the instructions I use when I make changes to a production config:

  • Create a new war file as below: ./apollo deploy.
  • Turn off tomcat and remove the old apollo directory and .war file in the webapps folder.
  • Copy in new .war file with the same name.
  • Restart tomcat and you are ready to go.


Nathan


On Jul 20, 2017, at 5:24 AM, Carolina Gandini <[hidden email]> wrote:

Hi Nathan,

yes, I have configured for blast. However, I do not understand which database extension I have to specify since the makeblastdb output is composed by 5 files. I wrote in the url the path to the database without extension, as I do with other programs but it did not work.

I am now making a new apollo.war with blat configuration. There is any way to change configuration without making a new .war?

Thanks,

Carolina

On Wed, Jul 19, 2017 at 12:40 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

Are you trying to setup blat or blast?  It looks like blast. 

If your binaries are pointing to the correct location then in the organism tab you specify the directory here (we have ours setup for blat):

<Screen Shot 2017-07-19 at 8.38.08 AM.png>

If you can I would recommend blat, but blast should work as well.

If you run into further errors, please provide the tomcat log (catalina.out) as well.  

Nathan


On Jul 18, 2017, at 6:26 PM, Carolina Gandini <[hidden email]> wrote:


Hi! the search tool is not working. My apollo-config file is the following:

// default username/password on h2 are given here. see docs for adjusting

dataSource {

    pooled = true

    jmxExport = true

    driverClassName = "org.h2.Driver"

    username = "[hidden email]"

    password = "1789"

}

// environment specific settings

environments {

    development {

        // sample config to turn on debug logging in development e.g. for apollo run-local

        log4j.main = {

            debug "grails.app"

        }

        // sample config to edit apollo specific configs in development mode

        apollo {

            gff3.source = "testing"

        }

        dataSource {

            dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }

    test {

        dataSource {

            dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''

            url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

        }

    }


    //note: not necessarily recommended to use h2 in production mode. see precautions

    production {

        dataSource {

            dbCreate = "update"

            //NOTE: production mode uses file instead of mem database

            //Please specify the appropriate file path, otherwise /tmp/prodDb will be used.

            //url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            url = "jdbc:h2:/tmp/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE"

            properties {

               // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation

               jmxEnabled = true

               initialSize = 5

               maxActive = 50

               minIdle = 5

               maxIdle = 25

               maxWait = 10000

               maxAge = 10 * 60000

               timeBetweenEvictionRunsMillis = 5000

               minEvictableIdleTimeMillis = 60000

               validationQuery = "SELECT 1"

               validationQueryTimeout = 3

               validationInterval = 15000

               testOnBorrow = true

               testWhileIdle = true

               testOnReturn = false

               jdbcInterceptors = "ConnectionState"

               defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED

            }

        }

    }



// default apollo settings

apollo {

  default_minimum_intron_size = 1

  history_size = 0

  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"

  track_name_comparator = "/config/track_name_comparator.js"

  use_cds_for_new_transcripts = true

  user_pure_memory_store = true

  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"

  is_partial_translation_allowed = false // unused so far

  get_translation_code = 11

  sequence_search_tools = [

  blat_nuc : [

          search_exe  : "/usr/local/ncbi/blast/bin/blastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast nucleotide",

          params      : ""

  ],

  blat_prot: [

          search_exe  : "/usr/local/ncbi/blast/bin/tblastn",

          search_class: "org.bbop.apollo.sequence.search.blast.BlastCommandLine",

          name        : "Blast protein to translated nucleotide",

          params      : ""

          //tmp_dir: "/opt/apollo/tmp" optional param

    ]

  ]    

     



  splice_donor_sites = [ "GT" ]

  splice_acceptor_sites = [ "AG"]

  gff3.source= "." bootstrap = false


  info_editor = {

    feature_types = "default"

    attributes = true

    dbxrefs = true

    pubmed_ids = true

    go_ids = true

    comments = true

  }

}


// Uncomment to make changes

//

jbrowse {

    git {

        url= "https://github.com/GMOD/jbrowse"

        tag = "1.12.2-apollo"

////        branch = "master"

        alwaysPull = true

        alwaysRecheck = true

    }

    plugins {

        WebApollo{

            included = true

        }

        NeatHTMLFeatures{

            included = true

        }

        NeatCanvasFeatures{

            included = true

        }

        RegexSequenceSearch{

            included = true

        }

        HideTrackLabels{

            included = true

        }

        MyVariantInfo {

            git = 'https://github.com/GMOD/myvariantviewer'

            branch = 'master'

            alwaysRecheck = "true"

            alwaysPull = "true"

        }

        SashimiPlot {

            git = 'https://github.com/cmdcolin/sashimiplot'

            branch = 'master'

            alwaysPull = "true"

        }

        BlastView {

            git = 'https://github.com/TAMU-CPT/blastview'

            branch = 'master'

            alwaysPull = "true"

        }

        SequenceViews {

            git = 'https://github.com/bhofmei/jbplugin-seqview'

            branch = 'master'

            alwaysPull = "true"

        }

    }

}

}


Which database I have to set as blast database? Do I have to add path to the makeblastdb output of my reference sequence?

Thanks in advance!

Carolina






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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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