Tripal installation: tripal_organism files in the wrong place?

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Tripal installation: tripal_organism files in the wrong place?

Collett, James R-2
Hello again,
 
I’m to the point in the Tripal Tutorial (v0.31b) installation process on Red at EL 6 where I’ve sync’d an organism (yeast) and now want to look at the organism page.  When I do so, I get multiple missing file errors, apparently for each file that is supposed to be found in ./sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/
 
warning: include(./sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/tripal_organism_feature_browser.tpl.php): failed to open stream: No such file or directory in /var/www/html/includes/theme.inc on line 1078.
 
I can cure this problem by creating soft links from  /var/www/html/sites/all/themes/theme_tripal/tripal_organism  (where the files actually are) to
/var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/ (where the files are supposed to be found according to the code in theme.inc, line 1078).
 
Have I misinstalled the tripal_organism files some how?
 
Is this anomaly related to this part in the tutorial, where the narrative says to copy the theme_tripal directory, but the move command (mv) is given?
“Next, we need to copy the Tripal base theme 'theme_tripal' directory to the /var/www/sites/all/themes directory so that Drupal can find it:”
“mv tripal-6.x-0.3.1b/theme_tripal /var/www/sites/all/themes”
 
I’m accessing the tutorial at http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b)
 
Thanks,
 
Jim
 
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
 
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN P8-60
Richland, WA  99352 USA
 
 

------------------------------------------------------------------------------
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Re: Tripal installation: tripal_organism files in the wrong place?

Stephen Ficklin-2
Hi Jim,

The tutorial has a mistype.  You are correct it says to "copy" but the command example given is "mv".   I updated the tutorial to correct this... it now says "move".  

The Tripal theme (named theme_tripal) should have all of the theming files you need (except for extension modules, which you'll come to later on).    If Drupal doesn't find the files in the theme directory then it typically means that the theme is not enabled.   Can you check to see if the the "Enable" checkbox on the Administer -> Site Building -> Themes for Tripal is checked? See the picture here:  http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b)#Enable_the_Tripal_Theme.  The default theme should be the Sky theme, but both should be enabled.

Also, make sure you have "base theme = tripal" at the bottom of the /var/www/sites/all/themes/sky/sky.info file.

Let me know if that helps.
Stephen



On 10/4/2011 7:05 PM, Collett, James R wrote:
Hello again,
 
I’m to the point in the Tripal Tutorial (v0.31b) installation process on Red at EL 6 where I’ve sync’d an organism (yeast) and now want to look at the organism page.  When I do so, I get multiple missing file errors, apparently for each file that is supposed to be found in ./sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/
 
warning: include(./sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/tripal_organism_feature_browser.tpl.php): failed to open stream: No such file or directory in /var/www/html/includes/theme.inc on line 1078.
 
I can cure this problem by creating soft links from  /var/www/html/sites/all/themes/theme_tripal/tripal_organism  (where the files actually are) to
/var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/ (where the files are supposed to be found according to the code in theme.inc, line 1078).
 
Have I misinstalled the tripal_organism files some how?
 
Is this anomaly related to this part in the tutorial, where the narrative says to copy the theme_tripal directory, but the move command (mv) is given?
“Next, we need to copy the Tripal base theme 'theme_tripal' directory to the /var/www/sites/all/themes directory so that Drupal can find it:”
“mv tripal-6.x-0.3.1b/theme_tripal /var/www/sites/all/themes”
 
I’m accessing the tutorial at http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b)
 
Thanks,
 
Jim
 
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
 
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN P8-60
Richland, WA  99352 USA
 
 


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1


_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Re: Tripal installation: tripal_organism files in the wrong place?

Collett, James R-2

It’s working now.  I had overlooked the instruction to append “base theme = tripal” to sky.info.  It was necessary to run update.php to get it to run correctly after editing sky.info.

 

Thanks,

 

Jim

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Tuesday, October 04, 2011 4:40 PM
To: [hidden email]
Subject: Re: [Gmod-tripal] Tripal installation: tripal_organism files in the wrong place?

 

Hi Jim,

The tutorial has a mistype.  You are correct it says to "copy" but the command example given is "mv".   I updated the tutorial to correct this... it now says "move".  

The Tripal theme (named theme_tripal) should have all of the theming files you need (except for extension modules, which you'll come to later on).    If Drupal doesn't find the files in the theme directory then it typically means that the theme is not enabled.   Can you check to see if the the "Enable" checkbox on the Administer -> Site Building -> Themes for Tripal is checked? See the picture here:  http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b)#Enable_the_Tripal_Theme.  The default theme should be the Sky theme, but both should be enabled.

Also, make sure you have "base theme = tripal" at the bottom of the /var/www/sites/all/themes/sky/sky.info file.

Let me know if that helps.
Stephen



On 10/4/2011 7:05 PM, Collett, James R wrote:

Hello again,

 

I’m to the point in the Tripal Tutorial (v0.31b) installation process on Red at EL 6 where I’ve sync’d an organism (yeast) and now want to look at the organism page.  When I do so, I get multiple missing file errors, apparently for each file that is supposed to be found in ./sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/

 

warning: include(./sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/tripal_organism_feature_browser.tpl.php): failed to open stream: No such file or directory in /var/www/html/includes/theme.inc on line 1078.

 

I can cure this problem by creating soft links from  /var/www/html/sites/all/themes/theme_tripal/tripal_organism  (where the files actually are) to

/var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/ (where the files are supposed to be found according to the code in theme.inc, line 1078).

 

Have I misinstalled the tripal_organism files some how?

 

Is this anomaly related to this part in the tutorial, where the narrative says to copy the theme_tripal directory, but the move command (mv) is given?

“Next, we need to copy the Tripal base theme 'theme_tripal' directory to the /var/www/sites/all/themes directory so that Drupal can find it:”

“mv tripal-6.x-0.3.1b/theme_tripal /var/www/sites/all/themes”

 

I’m accessing the tutorial at http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b)

 

Thanks,

 

Jim

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

 

 




------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1




_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

 


------------------------------------------------------------------------------
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Tripal installation tutorial: multi-fasta loader regular expression matching failure

Collett, James R-2

Hello,

 

I’m at the point in the Tripal installation tutorial where one attempts to load 3 kinds of fasta files and then match the data to a gff file.

 

The first two fasta files seemed to load okay, but the peptide file had errors relating to failure to match its features via regular expressions to the names of parent genes within the gff file.

 

Can you tell me what may have gone wrong?  I’m installing on Red Hat EL 6.

 

Here below is the summary of peptide file loading job, followed by stdout during the loading operation.

 

Thanks,

 

Jim

 

Job Description                 Import FASTA file: /var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt

Submitting Module         tripal_feature

Callback function              tripal_feature_load_fasta

Arguments        

FASTA file            /var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt

Organism             Drosophila melanogaster

Sequence Type peptide

Name Match Type           Unique name

Name RE              name=(.*?);

Unique Name RE              ID=(.*?);

Relationship Type            derives_from

Relationship Parent RE  parent=.*?,(.*?);

Relationship Parent Type             mRNA

Database Reference       FLyBase

Accession RE      ID=(.*?);

Method               Insert and update

Analysis                Drosophila melanogaster genes from Flybase

Progress              100%

Status   Completed

 

 

$ cd /var/www/html; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin

 

Tripal Job Launcher

-------------------

Calling: tripal_feature_load_fasta(/var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt, 2, peptide, , name=(.*?);, ID=(.*?);, ID=

(.*?);, 73, derives_from, parent=.*?,(.*?);, mRNA, Insert and update, 1, 10, Unique name, 15)

Opening FASTA file /var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt

Inserted feature Gpb5-PC (FBpp0112499)

WARNING: failed to find feature 'Gpb5-PC' ('FBpp0112499') while matching on unique name. Skipping

Inserted feature Gpb5-PA (FBpp0112500)

WARNING: failed to find feature 'Gpb5-PA' ('FBpp0112500') while matching on unique name. Skipping

Inserted feature CG12567-PA (FBpp0112427)

WARNING: failed to find feature 'CG12567-PA' ('FBpp0112427') while matching on unique name. Skipping

Inserted feature CG12567-PC (FBpp0112428)

WARNING: failed to find feature 'CG12567-PC' ('FBpp0112428') while matching on unique name. Skipping

Inserted feature CG12567-PD (FBpp0289926)

WARNING: failed to find feature 'CG12567-PD' ('FBpp0289926') while matching on unique name. Skipping

Inserted feature CG12567-PE (FBpp0289927)

WARNING: failed to find feature 'CG12567-PE' ('FBpp0289927') while matching on unique name. Skipping

Inserted feature CG12567-PF (FBpp0289928)

WARNING: failed to find feature 'CG12567-PF' ('FBpp0289928') while matching on unique name. Skipping

Inserted feature CG40042-PA (FBpp0112504)

WARNING: failed to find feature 'CG40042-PA' ('FBpp0112504') while matching on unique name. Skipping

Inserted feature CG40042-PD (FBpp0289594)

WARNING: failed to find feature 'CG40042-PD' ('FBpp0289594') while matching on unique name. Skipping

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

 

 

 


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Re: Tripal installation tutorial: multi-fasta loader regular expression matching failure

Stephen Ficklin-2
Hi Jim,

My apologies. It looks like there is a mistake in the tutorial.  It instructed you to enter the type 'peptide'  when importing the FASTA file with the protein sequences.  However, the protein sequences are present in the GFF file as type 'protein' and this is how they are imported into the database.  So, when you tried to import the protein sequences using type 'peptide' it tries to find the features with that type and it can't find them because they are of type 'protein' which is an alias in the sequence ontology for 'polypeptide'.   If you create a new FASTA import job and use the type 'protein'  I believe it will work for you.

I've updated the tutorial to correct the mistake.

Stephen

On 10/6/2011 1:51 AM, Collett, James R wrote:

Hello,

 

I’m at the point in the Tripal installation tutorial where one attempts to load 3 kinds of fasta files and then match the data to a gff file.

 

The first two fasta files seemed to load okay, but the peptide file had errors relating to failure to match its features via regular expressions to the names of parent genes within the gff file.

 

Can you tell me what may have gone wrong?  I’m installing on Red Hat EL 6.

 

Here below is the summary of peptide file loading job, followed by stdout during the loading operation.

 

Thanks,

 

Jim

 

Job Description                 Import FASTA file: /var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt

Submitting Module         tripal_feature

Callback function              tripal_feature_load_fasta

Arguments        

FASTA file            /var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt

Organism             Drosophila melanogaster

Sequence Type peptide

Name Match Type           Unique name

Name RE              name=(.*?);

Unique Name RE              ID=(.*?);

Relationship Type            derives_from

Relationship Parent RE  parent=.*?,(.*?);

Relationship Parent Type             mRNA

Database Reference       FLyBase

Accession RE      ID=(.*?);

Method               Insert and update

Analysis                Drosophila melanogaster genes from Flybase

Progress              100%

Status   Completed

 

 

$ cd /var/www/html; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin

 

Tripal Job Launcher

-------------------

Calling: tripal_feature_load_fasta(/var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt, 2, peptide, , name=(.*?);, ID=(.*?);, ID=

(.*?);, 73, derives_from, parent=.*?,(.*?);, mRNA, Insert and update, 1, 10, Unique name, 15)

Opening FASTA file /var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt

Inserted feature Gpb5-PC (FBpp0112499)

WARNING: failed to find feature 'Gpb5-PC' ('FBpp0112499') while matching on unique name. Skipping

Inserted feature Gpb5-PA (FBpp0112500)

WARNING: failed to find feature 'Gpb5-PA' ('FBpp0112500') while matching on unique name. Skipping

Inserted feature CG12567-PA (FBpp0112427)

WARNING: failed to find feature 'CG12567-PA' ('FBpp0112427') while matching on unique name. Skipping

Inserted feature CG12567-PC (FBpp0112428)

WARNING: failed to find feature 'CG12567-PC' ('FBpp0112428') while matching on unique name. Skipping

Inserted feature CG12567-PD (FBpp0289926)

WARNING: failed to find feature 'CG12567-PD' ('FBpp0289926') while matching on unique name. Skipping

Inserted feature CG12567-PE (FBpp0289927)

WARNING: failed to find feature 'CG12567-PE' ('FBpp0289927') while matching on unique name. Skipping

Inserted feature CG12567-PF (FBpp0289928)

WARNING: failed to find feature 'CG12567-PF' ('FBpp0289928') while matching on unique name. Skipping

Inserted feature CG40042-PA (FBpp0112504)

WARNING: failed to find feature 'CG40042-PA' ('FBpp0112504') while matching on unique name. Skipping

Inserted feature CG40042-PD (FBpp0289594)

WARNING: failed to find feature 'CG40042-PD' ('FBpp0289594') while matching on unique name. Skipping

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

 

 

 



------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1


_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
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Re: Tripal installation tutorial: multi-fasta loader regular expression matching failure

Collett, James R-2

Thanks, Stephen.

 

It appeared to load correctly this time.

 

Jim

 

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Thursday, October 06, 2011 5:49 PM
To: [hidden email]
Subject: Re: [Gmod-tripal] Tripal installation tutorial: multi-fasta loader regular expression matching failure

 

Hi Jim,

My apologies. It looks like there is a mistake in the tutorial.  It instructed you to enter the type 'peptide'  when importing the FASTA file with the protein sequences.  However, the protein sequences are present in the GFF file as type 'protein' and this is how they are imported into the database.  So, when you tried to import the protein sequences using type 'peptide' it tries to find the features with that type and it can't find them because they are of type 'protein' which is an alias in the sequence ontology for 'polypeptide'.   If you create a new FASTA import job and use the type 'protein'  I believe it will work for you.

I've updated the tutorial to correct the mistake.

Stephen

On 10/6/2011 1:51 AM, Collett, James R wrote:

Hello,

 

I’m at the point in the Tripal installation tutorial where one attempts to load 3 kinds of fasta files and then match the data to a gff file.

 

The first two fasta files seemed to load okay, but the peptide file had errors relating to failure to match its features via regular expressions to the names of parent genes within the gff file.

 

Can you tell me what may have gone wrong?  I’m installing on Red Hat EL 6.

 

Here below is the summary of peptide file loading job, followed by stdout during the loading operation.

 

Thanks,

 

Jim

 

Job Description                 Import FASTA file: /var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt

Submitting Module         tripal_feature

Callback function              tripal_feature_load_fasta

Arguments        

FASTA file            /var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt

Organism             Drosophila melanogaster

Sequence Type peptide

Name Match Type           Unique name

Name RE              name=(.*?);

Unique Name RE              ID=(.*?);

Relationship Type            derives_from

Relationship Parent RE  parent=.*?,(.*?);

Relationship Parent Type             mRNA

Database Reference       FLyBase

Accession RE      ID=(.*?);

Method               Insert and update

Analysis                Drosophila melanogaster genes from Flybase

Progress              100%

Status   Completed

 

 

$ cd /var/www/html; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin

 

Tripal Job Launcher

-------------------

Calling: tripal_feature_load_fasta(/var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt, 2, peptide, , name=(.*?);, ID=(.*?);, ID=

(.*?);, 73, derives_from, parent=.*?,(.*?);, mRNA, Insert and update, 1, 10, Unique name, 15)

Opening FASTA file /var/www/html/sites/default/files/Flybase-tripal-demo.peptides.fna.txt

Inserted feature Gpb5-PC (FBpp0112499)

WARNING: failed to find feature 'Gpb5-PC' ('FBpp0112499') while matching on unique name. Skipping

Inserted feature Gpb5-PA (FBpp0112500)

WARNING: failed to find feature 'Gpb5-PA' ('FBpp0112500') while matching on unique name. Skipping

Inserted feature CG12567-PA (FBpp0112427)

WARNING: failed to find feature 'CG12567-PA' ('FBpp0112427') while matching on unique name. Skipping

Inserted feature CG12567-PC (FBpp0112428)

WARNING: failed to find feature 'CG12567-PC' ('FBpp0112428') while matching on unique name. Skipping

Inserted feature CG12567-PD (FBpp0289926)

WARNING: failed to find feature 'CG12567-PD' ('FBpp0289926') while matching on unique name. Skipping

Inserted feature CG12567-PE (FBpp0289927)

WARNING: failed to find feature 'CG12567-PE' ('FBpp0289927') while matching on unique name. Skipping

Inserted feature CG12567-PF (FBpp0289928)

WARNING: failed to find feature 'CG12567-PF' ('FBpp0289928') while matching on unique name. Skipping

Inserted feature CG40042-PA (FBpp0112504)

WARNING: failed to find feature 'CG40042-PA' ('FBpp0112504') while matching on unique name. Skipping

Inserted feature CG40042-PD (FBpp0289594)

WARNING: failed to find feature 'CG40042-PD' ('FBpp0289594') while matching on unique name. Skipping

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

 

 

 




------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1




_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

 


------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
_______________________________________________
Gmod-tripal mailing list
[hidden email]
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