BLAT - Error running search

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BLAT - Error running search

Mirian Tsuchiya
Hi,

I'm running Apollo from AWS and almost everything is working fine, except for the sequence search. The error message I get is always:

Error running search: /data/blat/tmp/blat_tmp5233701561467953935

I have changed the tmp dir in apollo-config.groovy and also in grails-app/conf/Config.groovy. I have also created the folder blat is calling for (/data/blat/tmp/) without any luck. 

Is there anything else that needs to be done and I'm missing? I appreciate any help.

Thank you so much!
Best,
Mirian

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Re: BLAT - Error running search

nathandunn

Mirian,

Can you paste your apollo-config.groovy file (at least the blat configuration section?)

Also, do you have the blat binary loaded anywhere?

Thanks,

Nathan




> On Aug 9, 2019, at 8:05 AM, Mirian Tsuchiya <[hidden email]> wrote:
>
> Hi,
>
> I'm running Apollo from AWS and almost everything is working fine, except for the sequence search. The error message I get is always:
>
> Error running search: /data/blat/tmp/blat_tmp5233701561467953935
>
> I have changed the tmp dir in apollo-config.groovy and also in grails-app/conf/Config.groovy. I have also created the folder blat is calling for (/data/blat/tmp/) without any luck.
>
> Is there anything else that needs to be done and I'm missing? I appreciate any help.
>
> Thank you so much!
> Best,
> Mirian

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Re: BLAT - Error running search

Mirian Tsuchiya
Hi Nathan,
Thanks for he reply. 

Here's the apollo-config.groovy:

environments{

development{

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

    dataSource.username = "apollo2_user"

dataSource.password = "cEswUWr3br"

    dataSource.driverClassName = "org.postgresql.Driver"

    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect

    //dataSource.url = "jdbc:postgresql://localhost/apollo-release"

    dataSource.url = "jdbc:postgresql://localhost/apollo-release-production"

}

test{

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

    dataSource.username = "apollo2_user"

//    dataSource.password = "<CHANGEME>"

    dataSource.password = "cEswUWr3br"

    dataSource.driverClassName = "org.postgresql.Driver"

    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect

    dataSource.url = "jdbc:postgresql://localhost/apollo-release-test"

}

production{

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

    dataSource.username = "apollo2_user"

//    dataSource.password = "<CHANGEME>"

    dataSource.password = "cEswUWr3br"

    dataSource.driverClassName = "org.postgresql.Driver"

    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect

    dataSource.url = "jdbc:postgresql://localhost/apollo-release-production"

}

}



apollo{

sequence_search_tools {

blat_nuc {

    search_exe = "/home/ubuntu/miniconda2/bin/blat"

    search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide"

    name = "Blat nucleotide"

    params = "-minScore=0 -minMatch=1"

    tmp_dir = "/opt/apollo/data/blat/tmp"

}

blat_prot {

    search_exe = "/home/ubuntu/miniconda2/bin/blat"

    search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide"

    name = "Blat protein"

    params = "-minScore=0 -minMatch=1"

    tmp_dir = "/opt/apollo/data/blat/tmp"

}

}

}


And I install BLAT using conda. 

Thanks :)
Mirian

On Fri, Aug 9, 2019 at 11:35 AM Nathan Dunn <[hidden email]> wrote:

Mirian,

Can you paste your apollo-config.groovy file (at least the blat configuration section?)

Also, do you have the blat binary loaded anywhere?

Thanks,

Nathan




> On Aug 9, 2019, at 8:05 AM, Mirian Tsuchiya <[hidden email]> wrote:
>
> Hi,
>
> I'm running Apollo from AWS and almost everything is working fine, except for the sequence search. The error message I get is always:
>
> Error running search: /data/blat/tmp/blat_tmp5233701561467953935
>
> I have changed the tmp dir in apollo-config.groovy and also in grails-app/conf/Config.groovy. I have also created the folder blat is calling for (/data/blat/tmp/) without any luck.
>
> Is there anything else that needs to be done and I'm missing? I appreciate any help.
>
> Thank you so much!
> Best,
> Mirian

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Re: BLAT - Error running search

nathandunn

Does it work if your temp directory ends with a “/“?

    tmp_dir = "/opt/apollo/data/blat/tmp/"

Nathan


On Aug 9, 2019, at 8:36 AM, Mirian TN Tsuchiya <[hidden email]> wrote:

Hi Nathan,
Thanks for he reply. 

Here's the apollo-config.groovy:

environments{
development{
    dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
    dataSource.username = "apollo2_user"
dataSource.password = "cEswUWr3br"
    dataSource.driverClassName = "org.postgresql.Driver"
    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
    //dataSource.url = "jdbc:<a href="postgresql://localhost/apollo-release" class="">postgresql://localhost/apollo-release"
    dataSource.url = "jdbc:<a href="postgresql://localhost/apollo-release-production" class="">postgresql://localhost/apollo-release-production"
}
test{
    dataSource.dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
    dataSource.username = "apollo2_user"
//    dataSource.password = "<CHANGEME>"
    dataSource.password = "cEswUWr3br"
    dataSource.driverClassName = "org.postgresql.Driver"
    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
    dataSource.url = "jdbc:<a href="postgresql://localhost/apollo-release-test" class="">postgresql://localhost/apollo-release-test"
}
production{
    dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
    dataSource.username = "apollo2_user"
//    dataSource.password = "<CHANGEME>"
    dataSource.password = "cEswUWr3br"
    dataSource.driverClassName = "org.postgresql.Driver"
    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
    dataSource.url = "jdbc:<a href="postgresql://localhost/apollo-release-production" class="">postgresql://localhost/apollo-release-production"
}
}


apollo{
sequence_search_tools {
blat_nuc {
    search_exe = "/home/ubuntu/miniconda2/bin/blat"
    search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide"
    name = "Blat nucleotide"
    params = "-minScore=0 -minMatch=1"
    tmp_dir = "/opt/apollo/data/blat/tmp"
}
blat_prot {
    search_exe = "/home/ubuntu/miniconda2/bin/blat"
    search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide"
    name = "Blat protein"
    params = "-minScore=0 -minMatch=1"
    tmp_dir = "/opt/apollo/data/blat/tmp"
}
}
}

And I install BLAT using conda. 

Thanks :)
Mirian

On Fri, Aug 9, 2019 at 11:35 AM Nathan Dunn <[hidden email]> wrote:

Mirian,

Can you paste your apollo-config.groovy file (at least the blat configuration section?)

Also, do you have the blat binary loaded anywhere?

Thanks,

Nathan




> On Aug 9, 2019, at 8:05 AM, Mirian Tsuchiya <[hidden email]> wrote:
>
> Hi,
>
> I'm running Apollo from AWS and almost everything is working fine, except for the sequence search. The error message I get is always:
>
> Error running search: /data/blat/tmp/blat_tmp5233701561467953935
>
> I have changed the tmp dir in apollo-config.groovy and also in grails-app/conf/Config.groovy. I have also created the folder blat is calling for (/data/blat/tmp/) without any luck.
>
> Is there anything else that needs to be done and I'm missing? I appreciate any help.
>
> Thank you so much!
> Best,
> Mirian


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Re: BLAT - Error running search

Mirian Tsuchiya
No, It doesn't. :/ 

After changing it, is there any additional step I need to take? 
Also, the tmp dir on the error still appears as "/data/blat/tmp/blat_tmp970142245216170016". 

Thanks!

On Fri, Aug 9, 2019 at 11:39 AM Nathan Dunn <[hidden email]> wrote:

Does it work if your temp directory ends with a “/“?

    tmp_dir = "/opt/apollo/data/blat/tmp/"

Nathan


On Aug 9, 2019, at 8:36 AM, Mirian TN Tsuchiya <[hidden email]> wrote:

Hi Nathan,
Thanks for he reply. 

Here's the apollo-config.groovy:

environments{
development{
    dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
    dataSource.username = "apollo2_user"
dataSource.password = "cEswUWr3br"
    dataSource.driverClassName = "org.postgresql.Driver"
    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
    //dataSource.url = "jdbc:postgresql://localhost/apollo-release"
}
test{
    dataSource.dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
    dataSource.username = "apollo2_user"
//    dataSource.password = "<CHANGEME>"
    dataSource.password = "cEswUWr3br"
    dataSource.driverClassName = "org.postgresql.Driver"
    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
    dataSource.url = "jdbc:postgresql://localhost/apollo-release-test"
}
production{
    dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
    dataSource.username = "apollo2_user"
//    dataSource.password = "<CHANGEME>"
    dataSource.password = "cEswUWr3br"
    dataSource.driverClassName = "org.postgresql.Driver"
    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
}
}


apollo{
sequence_search_tools {
blat_nuc {
    search_exe = "/home/ubuntu/miniconda2/bin/blat"
    search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide"
    name = "Blat nucleotide"
    params = "-minScore=0 -minMatch=1"
    tmp_dir = "/opt/apollo/data/blat/tmp"
}
blat_prot {
    search_exe = "/home/ubuntu/miniconda2/bin/blat"
    search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide"
    name = "Blat protein"
    params = "-minScore=0 -minMatch=1"
    tmp_dir = "/opt/apollo/data/blat/tmp"
}
}
}

And I install BLAT using conda. 

Thanks :)
Mirian

On Fri, Aug 9, 2019 at 11:35 AM Nathan Dunn <[hidden email]> wrote:

Mirian,

Can you paste your apollo-config.groovy file (at least the blat configuration section?)

Also, do you have the blat binary loaded anywhere?

Thanks,

Nathan




> On Aug 9, 2019, at 8:05 AM, Mirian Tsuchiya <[hidden email]> wrote:
>
> Hi,
>
> I'm running Apollo from AWS and almost everything is working fine, except for the sequence search. The error message I get is always:
>
> Error running search: /data/blat/tmp/blat_tmp5233701561467953935
>
> I have changed the tmp dir in apollo-config.groovy and also in grails-app/conf/Config.groovy. I have also created the folder blat is calling for (/data/blat/tmp/) without any luck.
>
> Is there anything else that needs to be done and I'm missing? I appreciate any help.
>
> Thank you so much!
> Best,
> Mirian


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Re: BLAT - Error running search

nathandunn

Hmm . . usually you should have to redeploy with it.  

I’m not sure where you are getting the `tmp_dir = "/data/blat/tmp”` from as its not in your file, but it is what I deploy locally (not that it could influence that in any way).

Some quick questions:

1 - how are you deploying it?
2 - are there any more errors when you run the search?  It looks like there should be more that that.    Specifically are you getting additional errors in the server logs?  (catalina.out is  usually the file name)
3 - is there more to the config file?  

Thanks,


Nathan


> On Aug 9, 2019, at 8:42 AM, Mirian TN Tsuchiya <[hidden email]> wrote:
>
> No, It doesn't. :/
>
> After changing it, is there any additional step I need to take?
> Also, the tmp dir on the error still appears as "/data/blat/tmp/blat_tmp970142245216170016".
>
> Thanks!
>
> On Fri, Aug 9, 2019 at 11:39 AM Nathan Dunn <[hidden email]> wrote:
>
> Does it work if your temp directory ends with a “/“?
>
>    tmp_dir = "/opt/apollo/data/blat/tmp/"
>
> Nathan
>
>
>> On Aug 9, 2019, at 8:36 AM, Mirian TN Tsuchiya <[hidden email]> wrote:
>>
>> Hi Nathan,
>> Thanks for he reply.
>>
>> Here's the apollo-config.groovy:
>>
>> environments{
>> development{
>>    dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
>>    dataSource.username = "apollo2_user"
>> dataSource.password = "cEswUWr3br"
>>    dataSource.driverClassName = "org.postgresql.Driver"
>>    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
>>    //dataSource.url = "jdbc:postgresql://localhost/apollo-release"
>>    dataSource.url = "jdbc:postgresql://localhost/apollo-release-production"
>> }
>> test{
>>    dataSource.dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
>>    dataSource.username = "apollo2_user"
>> //    dataSource.password = "<CHANGEME>"
>>    dataSource.password = "cEswUWr3br"
>>    dataSource.driverClassName = "org.postgresql.Driver"
>>    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
>>    dataSource.url = "jdbc:postgresql://localhost/apollo-release-test"
>> }
>> production{
>>    dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
>>    dataSource.username = "apollo2_user"
>> //    dataSource.password = "<CHANGEME>"
>>    dataSource.password = "cEswUWr3br"
>>    dataSource.driverClassName = "org.postgresql.Driver"
>>    dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
>>    dataSource.url = "jdbc:postgresql://localhost/apollo-release-production"
>> }
>> }
>>
>>
>> apollo{
>> sequence_search_tools {
>> blat_nuc {
>>    search_exe = "/home/ubuntu/miniconda2/bin/blat"
>>    search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide"
>>    name = "Blat nucleotide"
>>    params = "-minScore=0 -minMatch=1"
>>    tmp_dir = "/opt/apollo/data/blat/tmp"
>> }
>> blat_prot {
>>    search_exe = "/home/ubuntu/miniconda2/bin/blat"
>>    search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide"
>>    name = "Blat protein"
>>    params = "-minScore=0 -minMatch=1"
>>    tmp_dir = "/opt/apollo/data/blat/tmp"
>> }
>> }
>> }
>>
>> And I install BLAT using conda.
>>
>> Thanks :)
>> Mirian
>>
>> On Fri, Aug 9, 2019 at 11:35 AM Nathan Dunn <[hidden email]> wrote:
>>
>> Mirian,
>>
>> Can you paste your apollo-config.groovy file (at least the blat configuration section?)
>>
>> Also, do you have the blat binary loaded anywhere?
>>
>> Thanks,
>>
>> Nathan
>>
>>
>>
>>
>> > On Aug 9, 2019, at 8:05 AM, Mirian Tsuchiya <[hidden email]> wrote:
>> >
>> > Hi,
>> >
>> > I'm running Apollo from AWS and almost everything is working fine, except for the sequence search. The error message I get is always:
>> >
>> > Error running search: /data/blat/tmp/blat_tmp5233701561467953935
>> >
>> > I have changed the tmp dir in apollo-config.groovy and also in grails-app/conf/Config.groovy. I have also created the folder blat is calling for (/data/blat/tmp/) without any luck.
>> >
>> > Is there anything else that needs to be done and I'm missing? I appreciate any help.
>> >
>> > Thank you so much!
>> > Best,
>> > Mirian
>>
>

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Re: BLAT - Error running search

nathandunn

Mirian,

The config file will be in your tomcat directory. 

So, typically wherever you’ve installed tomcat you drop in the .war file:

<path to tomcat>/webapps/apollo.war

The log file is usually in:

<path to tomcat>/logs/catalina.out 


(Sorry, l should have this in the help docs)



Nathan


On Aug 9, 2019, at 10:53 AM, Mirian TN Tsuchiya <[hidden email]> wrote:


So, I tried running apollo deploy, but it failed. So, I ran apollo clean-all and then apollo deploy and it worked. But the blat search still gives the same error. And that's the only error I have when running the search. But I don't have a catalina.out file in the apollo folder. Should it be somewhere else?
And yes, that was the entire config file.  

Thank you so much for your help.
Best,
Mirian



On Fri, Aug 9, 2019 at 12:56 PM Nathan Dunn <[hidden email]> wrote:

Hmm . . usually you should have to redeploy with it.   

I’m not sure where you are getting the `tmp_dir = "/data/blat/tmp”` from as its not in your file, but it is what I deploy locally (not that it could influence that in any way).

Some quick questions:

1 - how are you deploying it?
2 - are there any more errors when you run the search?  It looks like there should be more that that.    Specifically are you getting additional errors in the server logs?  (catalina.out is  usually the file name)
3 - is there more to the config file?   

Thanks,


Nathan


> On Aug 9, 2019, at 8:42 AM, Mirian TN Tsuchiya <[hidden email]> wrote:
>
> No, It doesn't. :/
>
> After changing it, is there any additional step I need to take?
> Also, the tmp dir on the error still appears as "/data/blat/tmp/blat_tmp970142245216170016".
>
> Thanks!
>
> On Fri, Aug 9, 2019 at 11:39 AM Nathan Dunn <[hidden email]> wrote:
>
> Does it work if your temp directory ends with a “/“?
>
>                   tmp_dir = "/opt/apollo/data/blat/tmp/"
>
> Nathan
>
>
>> On Aug 9, 2019, at 8:36 AM, Mirian TN Tsuchiya <[hidden email]> wrote:
>>
>> Hi Nathan,
>> Thanks for he reply.
>>
>> Here's the apollo-config.groovy:
>>
>> environments{
>>      development{
>>          dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
>>          dataSource.username = "apollo2_user"
>>      dataSource.password = "cEswUWr3br"
>>          dataSource.driverClassName = "org.postgresql.Driver"
>>          dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
>>          //dataSource.url = "jdbc:<a href="postgresql://localhost/apollo-release" class="">postgresql://localhost/apollo-release"
>>          dataSource.url = "jdbc:<a href="postgresql://localhost/apollo-release-production" class="">postgresql://localhost/apollo-release-production"
>>      }
>>      test{
>>          dataSource.dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
>>          dataSource.username = "apollo2_user"
>>      //    dataSource.password = "<CHANGEME>"
>>          dataSource.password = "cEswUWr3br"
>>          dataSource.driverClassName = "org.postgresql.Driver"
>>          dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
>>          dataSource.url = "jdbc:<a href="postgresql://localhost/apollo-release-test" class="">postgresql://localhost/apollo-release-test"
>>      }
>>      production{
>>          dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
>>          dataSource.username = "apollo2_user"
>>      //    dataSource.password = "<CHANGEME>"
>>          dataSource.password = "cEswUWr3br"
>>          dataSource.driverClassName = "org.postgresql.Driver"
>>          dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
>>          dataSource.url = "jdbc:<a href="postgresql://localhost/apollo-release-production" class="">postgresql://localhost/apollo-release-production"
>>      }
>> }
>>
>>
>> apollo{
>>      sequence_search_tools {
>>              blat_nuc {
>>                  search_exe = "/home/ubuntu/miniconda2/bin/blat"
>>                  search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide"
>>                  name = "Blat nucleotide"
>>                  params = "-minScore=0 -minMatch=1"
>>                  tmp_dir = "/opt/apollo/data/blat/tmp"
>>              }
>>              blat_prot {
>>                  search_exe = "/home/ubuntu/miniconda2/bin/blat"
>>                  search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide"
>>                  name = "Blat protein"
>>                  params = "-minScore=0 -minMatch=1"
>>                  tmp_dir = "/opt/apollo/data/blat/tmp"
>>              }
>>      }
>> }
>>
>> And I install BLAT using conda.
>>
>> Thanks :)
>> Mirian
>>
>> On Fri, Aug 9, 2019 at 11:35 AM Nathan Dunn <[hidden email]> wrote:
>>
>> Mirian,
>>
>> Can you paste your apollo-config.groovy file (at least the blat configuration section?)
>>
>> Also, do you have the blat binary loaded anywhere?
>>
>> Thanks,
>>
>> Nathan
>>
>>
>>
>>
>> > On Aug 9, 2019, at 8:05 AM, Mirian Tsuchiya <[hidden email]> wrote:
>> >
>> > Hi,
>> >
>> > I'm running Apollo from AWS and almost everything is working fine, except for the sequence search. The error message I get is always:
>> >
>> > Error running search: /data/blat/tmp/blat_tmp5233701561467953935
>> >
>> > I have changed the tmp dir in apollo-config.groovy and also in grails-app/conf/Config.groovy. I have also created the folder blat is calling for (/data/blat/tmp/) without any luck.
>> >
>> > Is there anything else that needs to be done and I'm missing? I appreciate any help.
>> >
>> > Thank you so much!
>> > Best,
>> > Mirian
>>
>


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Re: BLAT - Error running search

nathandunn
In reply to this post by nathandunn
Just for sharing. 

These pre-built and configured AWS instances (with data) should be up on the N. Virginia Community AMIs later today or tomorrow. 

Let me know if you have any trouble. 

Nathan


On Aug 13, 2019, at 10:06 AM, Nathan Dunn <[hidden email]> wrote:




As I just finished creating the Community AMI images for launching, I don’t think that they’ll be there until later today or tomorrow. 

Let me know if you have any trouble either way.

Nathan



On Aug 12, 2019, at 11:24 AM, Mirian TN Tsuchiya <[hidden email]> wrote:

Hey Nathan,
Thanks for the advice.

So, this all happened on an AWS instance. The perl libs were missing, and I had to install a bunch of things. Apollo deploy never worked, so it was a bit more confusing than I expected. But I also have limited experience with AWS, and I might have just over complicated things.

Anyway, I'll try the new instance and I'll let you know if I run into any issues. Thanks again for your patience.
Cheers,
Mirian

On Mon, Aug 12, 2019 at 2:18 PM Nathan Dunn <[hidden email]> wrote:


On Aug 12, 2019, at 11:02 AM, Mirian TN Tsuchiya <[hidden email]> wrote:

Yes, I tried to follow those.

But honestly, there we a lot of perl libs missing, and other things. I'm afraid I might have messed up things up. 

Yeah, these are annoying.  I usually have to do another apollo clean-all and that will help, but it is a pain. 

I'll try doing it locally first. Is it any different doing that from an aws instance?

If you can do it via AWS I would.   They are already setup, though you will need to upload your data.  


It looks like I’ve not updated 2.4, so I will need to do that, but 2.3.1 should be sufficient.   Let me know if not. 


The other option is to use docker, which will also pre-install everything on your machine. 

Let me know how those work.

Nathan

Thank you so much!
Mirian

On Mon, Aug 12, 2019 at 1:33 PM Nathan Dunn <[hidden email]> wrote:

Oh, these here? 


Yeah, make sure your instance is off and try installing with a new instance. 

Maybe even before you deploy to tomcat, make sure that tomcat is off and try running: `apollo run-local` with your configuration changes. 

You should connect to http://localhosthost:8080/apollo  and it should work (in theory). 

Nathan


On Aug 12, 2019, at 8:22 AM, Mirian TN Tsuchiya <[hidden email]> wrote:

Hi Nathan,
I hope you had a good weekend.

So, how did I install what, exactly? Tomcat? 
I installed tomcat following the read the docs instructions. 

I'm considering starting a new instance, just in case I did anything wrong and can't find it. 

Thanks,
Mirian

On Fri, Aug 9, 2019 at 4:19 PM Lbl <[hidden email]> wrote:

How did you install it and how are you running it? 

Nathan

On Aug 9, 2019, at 12:05 PM, Mirian TN Tsuchiya <[hidden email]> wrote:

Hi Nathan,
No problem.

So, I found tomcat at /usr/share/tomcat8, but there's not logs or webapps folder. Should I reinstall it?

Thank you so much for your patience!
best,
Mirian

On Fri, Aug 9, 2019 at 2:51 PM Nathan Dunn <[hidden email]> wrote:

Sorry, trying to respond as much in the Apollo list as possible so it will be useful to other folks. 

But if we need to take it offline, we can.

Thanks,

Nathan


On Aug 9, 2019, at 10:53 AM, Mirian TN Tsuchiya <[hidden email]> wrote:


So, I tried running apollo deploy, but it failed. So, I ran apollo clean-all and then apollo deploy and it worked. But the blat search still gives the same error. And that's the only error I have when running the search. But I don't have a catalina.out file in the apollo folder. Should it be somewhere else?
And yes, that was the entire config file.  

Thank you so much for your help.
Best,
Mirian



On Fri, Aug 9, 2019 at 12:56 PM Nathan Dunn <[hidden email]> wrote:

Hmm . . usually you should have to redeploy with it.   

I’m not sure where you are getting the `tmp_dir = "/data/blat/tmp”` from as its not in your file, but it is what I deploy locally (not that it could influence that in any way).

Some quick questions:

1 - how are you deploying it?
2 - are there any more errors when you run the search?  It looks like there should be more that that.    Specifically are you getting additional errors in the server logs?  (catalina.out is  usually the file name)
3 - is there more to the config file?   

Thanks,


Nathan


> On Aug 9, 2019, at 8:42 AM, Mirian TN Tsuchiya <[hidden email]> wrote:
>
> No, It doesn't. :/
>
> After changing it, is there any additional step I need to take?
> Also, the tmp dir on the error still appears as "/data/blat/tmp/blat_tmp970142245216170016".
>
> Thanks!
>
> On Fri, Aug 9, 2019 at 11:39 AM Nathan Dunn <[hidden email]> wrote:
>
> Does it work if your temp directory ends with a “/“?
>
>                   tmp_dir = "/opt/apollo/data/blat/tmp/"
>
> Nathan
>
>
>> On Aug 9, 2019, at 8:36 AM, Mirian TN Tsuchiya <[hidden email]> wrote:
>>
>> Hi Nathan,
>> Thanks for he reply.
>>
>> Here's the apollo-config.groovy:
>>
>> environments{
>>      development{
>>          dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
>>          dataSource.username = "apollo2_user"
>>      dataSource.password = "cEswUWr3br"
>>          dataSource.driverClassName = "org.postgresql.Driver"
>>          dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
>>          //dataSource.url = "jdbc:postgresql://localhost/apollo-release"
>>          dataSource.url = "jdbc:postgresql://localhost/apollo-release-production"
>>      }
>>      test{
>>          dataSource.dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
>>          dataSource.username = "apollo2_user"
>>      //    dataSource.password = "<CHANGEME>"
>>          dataSource.password = "cEswUWr3br"
>>          dataSource.driverClassName = "org.postgresql.Driver"
>>          dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
>>          dataSource.url = "jdbc:postgresql://localhost/apollo-release-test"
>>      }
>>      production{
>>          dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
>>          dataSource.username = "apollo2_user"
>>      //    dataSource.password = "<CHANGEME>"
>>          dataSource.password = "cEswUWr3br"
>>          dataSource.driverClassName = "org.postgresql.Driver"
>>          dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
>>          dataSource.url = "jdbc:postgresql://localhost/apollo-release-production"
>>      }
>> }
>>
>>
>> apollo{
>>      sequence_search_tools {
>>              blat_nuc {
>>                  search_exe = "/home/ubuntu/miniconda2/bin/blat"
>>                  search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide"
>>                  name = "Blat nucleotide"
>>                  params = "-minScore=0 -minMatch=1"
>>                  tmp_dir = "/opt/apollo/data/blat/tmp"
>>              }
>>              blat_prot {
>>                  search_exe = "/home/ubuntu/miniconda2/bin/blat"
>>                  search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide"
>>                  name = "Blat protein"
>>                  params = "-minScore=0 -minMatch=1"
>>                  tmp_dir = "/opt/apollo/data/blat/tmp"
>>              }
>>      }
>> }
>>
>> And I install BLAT using conda.
>>
>> Thanks :)
>> Mirian
>>
>> On Fri, Aug 9, 2019 at 11:35 AM Nathan Dunn <[hidden email]> wrote:
>>
>> Mirian,
>>
>> Can you paste your apollo-config.groovy file (at least the blat configuration section?)
>>
>> Also, do you have the blat binary loaded anywhere?
>>
>> Thanks,
>>
>> Nathan
>>
>>
>>
>>
>> > On Aug 9, 2019, at 8:05 AM, Mirian Tsuchiya <[hidden email]> wrote:
>> >
>> > Hi,
>> >
>> > I'm running Apollo from AWS and almost everything is working fine, except for the sequence search. The error message I get is always:
>> >
>> > Error running search: /data/blat/tmp/blat_tmp5233701561467953935
>> >
>> > I have changed the tmp dir in apollo-config.groovy and also in grails-app/conf/Config.groovy. I have also created the folder blat is calling for (/data/blat/tmp/) without any luck.
>> >
>> > Is there anything else that needs to be done and I'm missing? I appreciate any help.
>> >
>> > Thank you so much!
>> > Best,
>> > Mirian
>>
>






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