gmane.science.biology.galaxy.devel

writing tag in xml file for a C++ tool

vijayalakshmi — 2013-05-22T16:17:36

Hi all,

    I want to include a new tool to galaxy. The tool is written in C++. How
do I write the xml file to execute a cpp program?  The tool that I am
trying to integrate is    https://code.google.com/p/bedtools/

I have the class file to be executed and the command to execute it. For
example,

'IntersectBed' is my class file. The command to execute it is
    $intersectBed
-a reads.bed -b genes.bed   (reads.bed and genes.bed are input files
provided by the user)

How should I write the <command> tag in the xml file so as to execute the
above command? Since C++ is complied as opposed to Python which is
interpreted, I am not sure how to write the <command> tag.


I am a newbie. I appreciate any guidance offered!

Thanks,
VJ.

Run galaxy on a specific SGE queue

Sarah Maman — 2013-05-22T15:36:55

Hi everyone,
Galaxy is set up on our cluster, and so far everything is working just
fine. However, we'd like to change the submission queue from the default to
a specific one.

To do so, we tryed to set on the universe_wsgi.ini file the
default_cluster_job_runner parameter as following:
default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/

When doing so, an error occured telling us the job has been rejected
because 2 queues were specified: the workq (default one) and the test.q.
Should be the queue setting this way ? What are we doing wrong ?

thanks for your help,
Sarah

Re: Cross Tool Shed dependencies / blast_datatypes

Greg Von Kuster — 2013-05-22T20:59:17

I cannot guarantee it, but this may be related to a fix I just committed that populates the <repository> tag in the dependency definitions with a toolshed attribute if it is missing (it looks like it is in your case).  I used to not populate the tag, but simply stored the tool shed in the repository metadata.  Bjorn discovered, however, that certain repository installations would not succeed if the toolshed attribute was missing.  WHen I investigated this, I discovered  that some downstream stuff could not locate the appropriate tool shed if the attribute was missing from the tag.

I fixed this in 9836:252027d00b44 by populating this tag attribute if it was missing.  Unfortunately, a new dependency definition has to be uploaded to those repositories that have definitions where it is not set in order to get this fix.  

I don't know if updating your dependency file in this repository will fix this issue, but just wanted to alert you to this.

Very sorry for any inconvenience!

Greg Von Kuster


On May 22, 2013, at 4:26 PM, Peter Cock wrote:

Re: Cross Tool Shed dependencies / blast_datatypes

Peter Cock — 2013-05-22T20:26:06

On Mon, May 20, 2013 at 3:05 PM, Peter Cock <p.j.a.cock-gM/Ye1E23mwN+BqQ9rBEUg< at >public.gmane.org>
wrote:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bf634ebee84c
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/2d4757de6180

Hi Greg (& Dave),

Thanks for Dave for fixing the missing test results issue,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014791.html

I can now see the effect the dependency change had -
unfortunately the blast_datatypes install seems to be
unsuccessful, but I am not seeing a helpful error from
the Tool Shed tests.

Let's focus on the simplest case, where blast_datatypes
is the only dependency:

<?xml version="1.0"?>
<repositories description="This requires the BLAST datatype
definitions (e.g. the BLAST XML format).">
<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which
added BLAST databases -->
<repository name="blast_datatypes" owner="devteam"
changeset_revision="f9a7783ed7b6" />
</repositories>

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bf634ebee84c

Automated tool test results

Tool test results<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&id=90191ce08fa7fc29&message=&changeset_revision=bf634ebee84c>
Automated test environment<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&id=90191ce08fa7fc29&message=&changeset_revision=bf634ebee84c>
*Time tested:* ~ 6 hours ago*System:* Linux 3.5.0-21-generic*Architecture:*
 x86_64*Python version:* 2.7.3*Galaxy revision:* 9821:feaab01c738a*Galaxy
database version:* 115*Tool shed revision:* 9820:f5fe2f094060*Tool shed
database version:* 19*Tool shed mercurial version:* 2.2.3
Installation errors* - no functional tests were run for any tools in this
changeset revision*<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&id=90191ce08fa7fc29&message=&changeset_revision=bf634ebee84c>
Repository dependencies<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&id=90191ce08fa7fc29&message=&changeset_revision=bf634ebee84c>
Tool shedNameOwnerChangeset revisiontesttoolshed.g2.bx.psu.edu
blastxml_to_top_descrpeterjcbf634ebee84cErrorNone




It seems that an error occurred with the dependencies, but
unfortunately all we get as the error message is "None".

Regards,

Peter

Re: Missing test results on (Test) Tool Shed

Peter Cock — 2013-05-22T19:05:03

Looks good - and now I have some more errors to sort out :)

Thank you,

Peter

Re: Test Tool Shed still running tests marked as skip?

Dave Bouvier — 2013-05-22T17:48:49

Peter,

Thank you for reporting this issue, it has been resolved in 
9827:2a630237801f.

    --Dave B.

On 5/21/13 06:10:34.000, Peter Cock wrote:

Re: Missing test results on (Test) Tool Shed

Dave Bouvier — 2013-05-22T17:47:18

Peter,

I have implemented a system that will explicitly exclude a defined list 
of repositories from the testing framework, so your repositories' tests 
should now be running.

    --Dave B.

On 5/21/13 06:26:56.000, Peter Cock wrote:

populating the pull-down menu: reference genomes(built-in index)

Staheli, Jeannette — 2013-05-22T17:45:00

Hi,
We are trying to put a few reference genomes into the built-in index for bwa, bowtie, bowtie2 and tophat.  For the human hg19 we can find those.  However, we also like to upload the Rhesus macaque genome and haven't been able to find an indexed version at NCBI or other places.

Are other genomes pre-indexed for these applications somewhere?
How do those files look like exactly (extensions, number of files needed, etc.)?
How would we index the Rhesus genome for the above mappers if they are not available in an indexed form?

Thank you,
Jeannette

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Re: tag in xml file for a C++ tool

James Taylor — 2013-05-22T16:26:36

You might find it instructive to look at the existing bedtools wrappers here:

  http://toolshed.g2.bx.psu.edu/view/aaronquinlan/bedtools

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Wed, May 22, 2013 at 12:21 PM, vijayalakshmi <vs49-LjRBWs/Th6SVc3sceRu5cw< at >public.gmane.org> wrote:

Re: tag in xml file for a C++ tool

Peter Cock — 2013-05-22T16:25:30

For a compiled binary there is no interpreter, just use <command>. e.g.

<command>IntersectBed -a $inputreads -b $inputgenes ...</command>

I presume there are more options to your command, e.g. output files ;)

Peter

tag in xml file for a C++ tool

vijayalakshmi — 2013-05-22T16:21:01

Hi all,

    I want to include a new tool to galaxy. The tool is written in C++. How
do I write the xml file to execute a cpp program?  The tool that I am
trying to integrate is    https://code.google.com/p/bedtools/

I have the class file to be executed and the command to execute it. For
example,

'IntersectBed' is my class file. The command to execute it is
    $intersectBed
-a reads.bed -b genes.bed   (reads.bed and genes.bed are input files
provided by the user)

How should I write the <command> tag in the xml file so as to execute the
above command? Since C++ is complied as opposed to Python which is
interpreted, I am not sure how to write the <command> tag.


I am a newbie. I appreciate any guidance offered!

Thanks,
VJ.

Re: nginx Proxy to VM problem

Michael E. Cotterell — 2013-05-22T15:24:00

That's not the only thing I changed. I also have the following in my nginx conf file:

proxy_set_header Host $host;

instead of X-Forwarded-Host $host 

Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
mepcotterell-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org (mailto:mepcotterell-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org)
mepcott-zyaWFcxYZ9U< at >public.gmane.org (mailto:mepcott-zyaWFcxYZ9U< at >public.gmane.org)
mec-SIUyJ6YeNdM3uPMLIKxrzw< at >public.gmane.org (mailto:mec-SIUyJ6YeNdM3uPMLIKxrzw< at >public.gmane.org)
http://michaelcotterell.com/


On Wednesday, May 22, 2013 at 11:11 AM, Michael E. Cotterell wrote:

Re: nginx Proxy to VM problem

Michael E. Cotterell — 2013-05-22T15:11:01

I actually fixed the problem by not setting the cookie prefix in the ini file. Weird. 


Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
mepcotterell-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org (mailto:mepcotterell-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org)
mepcott-zyaWFcxYZ9U< at >public.gmane.org (mailto:mepcott-zyaWFcxYZ9U< at >public.gmane.org)
mec-SIUyJ6YeNdM3uPMLIKxrzw< at >public.gmane.org (mailto:mec-SIUyJ6YeNdM3uPMLIKxrzw< at >public.gmane.org)
http://michaelcotterell.com/


On Wednesday, May 22, 2013 at 9:51 AM, Michael E. Cotterell wrote:

nginx Proxy to VM problem

Michael E. Cotterell — 2013-05-22T13:51:35

Hey everyone, 

I'm having a weird login problem (think it's cookie related) after setting up Galaxy on a virtual machine and trying to proxy_pass to it using nginx. It says I'm logged in, but when I get redirected to the front page I'm no longer logged in. When I visit subsequent pages I'm also not logged in.

On the server, here is the relevant part of my nginx configuration (I'm going to setup static serving after I get the login issue resolved):

upstream galaxy_app {
  server 192.168.1.11:8080;
}


server {
  ...
  location /galaxy {
    proxy_pass http://galaxy_app;
    proxy_set_header X-Forwarded-Host $host;
    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
  }


  ...
}

The dots just mean that I have other things in there for the forwarding I do with other VMs. 

On the VM, in my universe_wsgi.ini file, I have made sure to set the following (just showing the parts I think are relevant):

[server:main]
port = 8080
host = 0.0.0.0

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy



[app:main]
filter-with = proxy-prefix
cookie_path = /galaxy

I should note that I might end up changing this configuration to use a CNAME at some point (thus avoiding the prefix issue), but for now I'm totally lost as to why I'm not able to login using my current configuration.

Any ideas?

Thanks! 

Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA & TA, University of Georgia
mepcotterell-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org (mailto:mepcotterell-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org)
mepcott-zyaWFcxYZ9U< at >public.gmane.org (mailto:mepcott-zyaWFcxYZ9U< at >public.gmane.org)
mec-SIUyJ6YeNdM3uPMLIKxrzw< at >public.gmane.org (mailto:mec-SIUyJ6YeNdM3uPMLIKxrzw< at >public.gmane.org)
http://michaelcotterell.com/

Problem with ftp connexion to Galaxy

Fabrice BESNARD — 2013-05-22T13:34:36

Hello,

I am a new Galaxy User.
I am definitely not an expert in informatics, so my questions may sound
silly to you... I apologize if it is the case!
Anyway, I cound not establish a ftp connexion to Galaxy through Filezilla,
and the error message suggests that it comes from an incorrect password to
Galaxy.

Here is the messages displayed by Filezilla (french version) while trying
to connnect:

Statut :Résolution de l'adresse de main.g2.bx.psu.edu
Statut :Connexion à 128.118.250.4:21...
Statut :Connexion établie, attente du message d'accueil...
Réponse :220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP)
[::ffff:128.118.250.4]
Commande :USER fbesnard-CrNPMedtCwFFYcqGaMRPHA< at >public.gmane.org
Réponse :331 Password required for fbesnard-CrNPMedtCwFFYcqGaMRPHA< at >public.gmane.org
Commande :PASS ***************
Réponse :530 Login incorrect.
Erreur :Erreur critique
Erreur :Impossible d'établir une connexion au serveur

I was puzzled by this error message, because I do connect as user in the
Galaxy website. As recommended, I use the SAME login (=email
adress)/Password in both Galaxy login page and filezilla.
I tried to reset my password and connect again: I could connect directly
to the web site, but I still failed establishing a connexion via
filezilla.

I just created an account yesterday to Galaxy (Tuesday, 21th of May 2013).
Maybe I should just wait a little bit for a synchronization of the user
connexion parameters, should I?

Moreover, my Filezilla is working with other ftp server, so that I think
we can exclude that the problem comes from there.

I extensively looked for similar trouble reports on internet (googling
with other terms "530 Login incorrect"). Unfortunately, I could not solve
this problem. However, I found that you were asked one year ago for a
similar problem in this page:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-July/010457.html But I
must confess that I could not understand most of what was written in this
informatic experts discussion! By the way, my system is not an ubuntu, so
I think that the solution you suggested would not work in my case.

Here are the characteristics and versions of the systems installed on my
computer:
Operating system: Windows 7 professionnal, 64bits
Filezilla Client 3.7.0.1
Firefox 20.0.1

I really thank you for reading this help message and I hope that you could
explain me how to solve my problem.

I look forward to reading your answer soon,
Best regards,

Re: Samtools and idxstats

Jeremy Goecks — 2013-05-22T13:39:13

Galaxy stores a BAI for each BAM internally; you can access it in a tool wrapper like this (assuming the name of your input dataset is 'input_bam':

${input_bam.metadata.bam_index}

Once you have the file path, you can set up a symbolic link to it and the tool should work fine.

Good luck,
J.



On May 22, 2013, at 4:05 AM, Michiel Van Bel wrote:

Samtools and idxstats

Michiel Van Bel — 2013-05-22T08:05:35

Hi,

I would like to inquire whether anyone has attempted to implement the 
idxstats tool from samtools into Galaxy?
The xml-file for idxstats is not present in the Galaxy source code, 
which led me to try and implement it myself.
However, the main problem I face is that the idxstats tool silently 
relies on having an index file available (within the same directory)  
for the bam file you which to print the stats for.
E.g. 
samtools idxstats PATH/test.bam
searches for PATH/test.bam.bai  and gives an error when this file is not 
present. And somehow I cannot model this behavior in Galaxy.

A different solution would of course be to ask the author(s) of samtools 
to have an option available where the user can directly indicate the 
path to the index file.

regards,
Michiel

PS: I've searched the mailing list archives for this problem but did not 
find any matches. Apologies if I somehow missed the answer.

Re: location of .loc-files/data tables -- bug orfeature?

Christian Hundsrucker — 2013-05-22T07:33:41

Hey Dannon,

thnx for the info and the quick reply!

On 21.05.2013 18:09, Dannon Baker wrote:

Re: import Workflow from public Galaxy to localinstance

Dannon Baker — 2013-05-22T11:57:56

On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk <
andreas.kuntzagk-weD559QjsLDQLMG2gba6HQ< at >public.gmane.org> wrote:


If you click on that link above, you can see the id in the url for the
'Import' link.  Again, definitely not optimal -- public workflows should
probably all be exposed via the API for use/import.

Re: import Workflow from public Galaxy to localinstance

Andreas Kuntzagk — 2013-05-22T07:12:15

Hi,

On 21.05.2013 18:06, Dannon Baker wrote:

I wanted to avoid that since I have to import more then one workflow.


But how do I get the workflow_id? For example for the workflow
https://main.g2.bx.psu.edu/u/gm2123/w/cloudmap-unmapped-mutant-workflow-no-candidates

what would the workflow_id be?
(I tried "cloudmap-unmapped-mutant-workflow-no-candidates" but this did not work.)

regards, Andreas

Re: workflow startup issues

Geert Vandeweyer — 2013-05-22T06:04:37

Aside: If I add steps to the beginning of the workfow, the step that 
runs too early, typically occurs earlier in the flow. Can this indicate 
a race condition where not all dependencies are available (stored?) yet 
in the database at the time of querying for job eligible for queueing?

Best,

Geert

On 05/21/2013 11:06 PM, Geert Vandeweyer wrote: