Re: [galaxy-dev] Script which creates users

2011-06-01 Thread Chorny, Ilya
Can someone point me to the script that adds users to the user database? I want to check to see if a linux user name exists and add create that account if it doesn't. BTW, has anyone else implemented this? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern

Re: [galaxy-dev] Passing username to drmaa.py

2011-06-08 Thread Chorny, Ilya
I am trying to figure out how to pass the current user name to drama.py. I have had little success so far. None of the environmental variables contain any current user information. Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern

Re: [galaxy-dev] Passing username to drmaa.py

2011-06-14 Thread Chorny, Ilya
9:47 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Passing username to drmaa.py Chorny, Ilya wrote: I am trying to figure out how to pass the current user name to drama.py. I have had little success so far. None of the environmental variables contain any

Re: [galaxy-dev] Passing username to drmaa.py

2011-06-15 Thread Chorny, Ilya
I found the statement in __init__.py but not in upload_common.py. Thanks, Ilya -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Wednesday, June 15, 2011 8:47 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Passing username to drmaa.py

Re: [galaxy-dev] Setting up Galaxy with SGE

2011-06-15 Thread Chorny, Ilya
Ravi, Do your galaxy jobs submit to the cluster as the galaxy user or as the user? Thanks, Ilya Sent from my iPhone On Jun 15, 2011, at 2:43 PM, Ravi Madduri madd...@mcs.anl.govmailto:madd...@mcs.anl.gov wrote: Hi We have been able to get the following setup working pretty reliably: *

Re: [galaxy-dev] TopHat V1.1 with GTF files

2011-07-11 Thread Chorny, Ilya
I figured it out. Please disregard my last email. Thanks, Ilya From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Monday, July 11, 2011 10:00 AM To: galaxy-dev@lists.bx.psu.edu; galaxy-user-boun...@lists.bx.psu.edu Subject

[galaxy-dev] Newer Version of Cufflinks Wrapper

2011-07-20 Thread Chorny, Ilya
Has anyone produced a newer version of the cufflinks wrapper? The current wrapper is for version 0.9.1. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern icho...@illumina.commailto:icho...@illumina.com 858-202-4582 ___ Please keep

[galaxy-dev] Scroll bars not present using i.e.

2011-07-22 Thread Chorny, Ilya
http://test.g2.bx.psu.edu/ Cheers, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern icho...@illumina.commailto:icho...@illumina.com 858-202-4582 ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] Newer Version of Cufflinks Wrapper

2011-07-22 Thread Chorny, Ilya
. Thanks, J. On Jul 21, 2011, at 5:16 PM, Chorny, Ilya wrote: I would be happy to share any changes that I make. By patch do you mean a diff/patch share patch or just check in the code? From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Wednesday, July 20, 2011 4:55 PM To: Chorny, Ilya Cc

[galaxy-dev] set_matadata_externally =True

2011-07-25 Thread Chorny, Ilya
I am still working on the patch to submit jobs as the actual user under SGE . I have it working for the default case but it fails for the case of set_metadata_externally = TRUE. Can someone point me to where the metadata files are created so that I can change the permissions for those files?

Re: [galaxy-dev] galaxy sge Job output not returned from cluster

2011-07-26 Thread Chorny, Ilya
Those changes to permission in __init__.py are only necessary of running the job as the actual logged in user and not as the galaxy user. There are additional changes that are needed to get actual user name integration to work with SGE. From: galaxy-dev-boun...@lists.bx.psu.edu

Re: [galaxy-dev] set_metadata_externally =True

2011-07-27 Thread Chorny, Ilya
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Monday, July 25, 2011 4:29 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] set_matadata_externally =True I am still working on the patch to submit jobs as the actual user under SGE . I have it working for the default case

[galaxy-dev] Regarding submitting jobs as actual user

2011-07-27 Thread Chorny, Ilya
I completed the changes to galaxy to submit DRMAA jobs (SGE) as the actual galaxy user. You can see the code at the fork below. Below is a brief description of how to turn it which is also described in the universe_wsgi.ini.sample. https://icho...@bitbucket.org/ichorny/galaxy-central #

[galaxy-dev] Updated Cufflinks Wrapper

2011-07-27 Thread Chorny, Ilya
I made some changes to the cufflinks wrapper. I added the -g/--GTF-guide use reference transcript annotation to guide assembly as an option. The version number needs to still be updated in my commit. https://bitbucket.org/ichorny/galaxy-central/changeset/fc5e24d453e5 Ilya Chorny Ph.D.

[galaxy-dev] dataset_*_file directory being compied to file_path when running fastqc

2011-07-28 Thread Chorny, Ilya
I am testing the latest galaxy central distribution by running FASTQC. It creates a directory call dataset_*_file in the job_working_directory and then copies that directory to file_path when the job is complete. Is that on purpose or is that a bug? Thanks, Ilya Ilya Chorny Ph.D.

Re: [galaxy-dev] dataset_*_file directory being compied to file_path when running fastqc

2011-07-28 Thread Chorny, Ilya
Thanks, that makes sense. Ilya -Original Message- From: Ross [mailto:ross.laza...@gmail.com] Sent: Thursday, July 28, 2011 10:14 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] dataset_*_file directory being compied to file_path when running fastqc It's

[galaxy-dev] upload.py fails with files having commas in file name

2011-07-29 Thread Chorny, Ilya
The ftp upload module fails when a file has a comma in the file name for example test.bam works but when copied to test,test.bam that file fails. Cheers, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern icho...@illumina.commailto:icho...@illumina.com 858-202-4582

[galaxy-dev] collect_associated_files and umask

2011-07-29 Thread Chorny, Ilya
When I run galaxy as the actual user using the code I committed to my fork, I run into a problem with dataset_*.dat files that have associated data wherein the associated data files are copied from the job_working_directory into the files directory. That directory is owned by the actual user

[galaxy-dev] When writing wrapper do not use shutil.copy()

2011-08-19 Thread Chorny, Ilya
If possible when writing wrappers do not use shutil.copy() when copying a file to a dataset_(job_id).dat file. shutil.copy() tries to change the permission of the copied to file. Better to use shutil.copyfile(). Ilya Chorny Ph.D. Bioinformatics - Intern

Re: [galaxy-dev] database/files/_metadata_files

2011-08-23 Thread Chorny, Ilya
Great, thanks!! From: Daniel Blankenberg [mailto:d...@bx.psu.edu] Sent: Tuesday, August 23, 2011 1:26 PM To: Chorny, Ilya Subject: Re: [galaxy-dev] database/files/_metadata_files Run a tool (or auto-detect metadata) that creates any BAM or MAF output file. The file will originally be created

[galaxy-dev] What script updates the umask of database/files/* and deletes database/job_working_directory

2011-08-23 Thread Chorny, Ilya
When running as the actual user in drama, I made it so the .dat files are not initially created so that when a tool moves data from the a temp directory to the out .dat file it will not fail. (i.e. unix does not allow moving a file owned by one user to a file owned by another user because mv

Re: [galaxy-dev] What script updates the umask of database/files/* and deletes database/job_working_directory

2011-08-23 Thread Chorny, Ilya
. Thoughts? Thanks, Ilya From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Tuesday, August 23, 2011 1:46 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] What script updates the umask of database/files/* and deletes database

[galaxy-dev] Metadata error

2011-08-23 Thread Chorny, Ilya
I get these two error in the log file. The job finishes correctly and a metadata file is created but I still get the error. Can anyone provide me with more detail about what this error means? The second error is incorrect because the files were deleted. setting metadata externally failed for

[galaxy-dev] upload multiple files

2011-08-24 Thread Chorny, Ilya
I noticed that when uploading multiple files only one job gets submitted to the queue. Is there a way for galaxy to split that up on multiple nodes? Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email:

Re: [galaxy-dev] Updated Cufflinks Wrapper

2011-08-25 Thread Chorny, Ilya
were trying to do. Let us know if you have any questions. Best, J. On Jul 27, 2011, at 7:26 PM, Chorny, Ilya wrote: I made some changes to the cufflinks wrapper. I added the -g/--GTF-guide use reference transcript annotation to guide assembly as an option. The version number needs to still

[galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread Chorny, Ilya
This is probably a question for our sys admin but when I run tools such as GATK I get an error java command not found. I can execute java from the command line and it works. Further I can grab the drmaa submission script (ie galaxy_job_id.sh) and qsub it from the command line and it finds

Re: [galaxy-dev] Tools requiring java can't find java

2011-08-30 Thread Chorny, Ilya
How do I set my path in a non login shell? From: George Marselis [mailto:george.marse...@kaust.edu.sa] Sent: Tuesday, August 30, 2011 9:40 AM To: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tools requiring java can't find java Yes, your java path is not set, because you

Re: [galaxy-dev] TEMP variable in cluster install

2011-09-02 Thread Chorny, Ilya
Nate, We ran into this issue with /tmp not having enough space. We came up with a generic solution and were wondering if you might want to add it to galaxy-central. We did not want to modify SGE as it could affect other jobs that use the cluster. We created a TMPDIR option in

Re: [galaxy-dev] TEMP variable in cluster install

2011-09-06 Thread Chorny, Ilya
: Tuesday, September 06, 2011 7:21 AM To: Chorny, Ilya Cc: Assaf Gordon; Shantanu Pavgi; galaxydev psu Subject: Re: [galaxy-dev] TEMP variable in cluster install Chorny, Ilya wrote: Nate, We ran into this issue with /tmp not having enough space. We came up with a generic solution and were

[galaxy-dev] cuffcompare wrapper

2011-09-07 Thread Chorny, Ilya
Hi Jeremy, The symlink in the cuffcompare wrapper was causing galaxy to crash because I run as the actual user and have to chmod the job_working directory at the end so Galaxy can clean it up. Turns out is seems like the symlink is not needed. Am I missing something. See below. Your code: for

Re: [galaxy-dev] GATK Unified Genotyper

2011-09-07 Thread Chorny, Ilya
Hi Daniel, I have been implementing the GATK unified genotyper and I was having some issues. Occasionally I would get an error that the Java virtual machine would not start. I got around that by adding the Xmx3g parameter to the command line. I also added the -nt 3 because otherwise it's

Re: [galaxy-dev] cuffcompare wrapper

2011-09-07 Thread Chorny, Ilya
...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Wednesday, September 07, 2011 9:18 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] cuffcompare wrapper Hi Jeremy, The symlink in the cuffcompare wrapper was causing galaxy to crash because I run as the actual user and have to chmod

Re: [galaxy-dev] cuffcompare wrapper

2011-09-08 Thread Chorny, Ilya
07, 2011 6:26 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cuffcompare wrapper Ilya, A search of the Galaxy codebase indicates that thirteen tools use symlinks (e.g. GATK, Sicer, Picard, Cuff*, Bowtie), so the changes required to support this new code

Re: [galaxy-dev] macs in galaxy

2011-09-08 Thread Chorny, Ilya
Is there a python script associated with the macs.xml file? From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kanwei Li Sent: Wednesday, August 24, 2011 5:41 PM To: KOH Jia Yu Jayce Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] macs

[galaxy-dev] Passing the number of mpi processors to SGE from xml file

2011-09-13 Thread Chorny, Ilya
Any thoughts on how to pass the number of processor I want to use from my xml wrapper to the job template. I am trying to wrap pBWA and use mpi. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email:

Re: [galaxy-dev] Passing the number of mpi processors to SGE from xml file

2011-09-14 Thread Chorny, Ilya
Nate, Any thoughts on how to do this? Can I add an xml tag that gets parsed and set's -PE mpi $NSLOTS in the job template. Can you point me to where the xml get's parsed? Thanks, Ilya From: Glen Beane [mailto:glen.be...@jax.org] Sent: Tuesday, September 13, 2011 5:00 PM To: Chorny, Ilya

Re: [galaxy-dev] Passing the number of mpi processors to SGE from xml file

2011-09-14 Thread Chorny, Ilya
It's easy to hard code in the ini but I want to be able to set the number of processors as a parameter. From: Glen Beane [mailto:glen.be...@jax.org] Sent: Wednesday, September 14, 2011 10:34 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Passing the number of mpi

Re: [galaxy-dev] use_tasked_jobs

2011-09-23 Thread Chorny, Ilya
. -Dannon On Sep 20, 2011, at 6:58 PM, Chorny, Ilya wrote: Hi Nate, We are having an issue that when use_tasked_jobs = True, the job_wrapper.user = None in drama.py. Do you know why that might be. It crashes my code. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I

Re: [galaxy-dev] use_tasked_jobs

2011-09-23 Thread Chorny, Ilya
: -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Friday, September 23, 2011 4:18 AM To: Chorny, Ilya Cc: Nate Coraor (n...@bx.psu.edu); galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] use_tasked_jobs TaskWrapper should inherit it from JobWrapper, so I just removed

[galaxy-dev] use_tasked_jobs and drmaa

2011-09-23 Thread Chorny, Ilya
So we have some new issues with use_tasked_jobs and drama and wanted to share with the community. 1.)The task get split on the head node which will bog down the head node if multiple user submit a job which requires splitting. It would be great if we could submit that to drmaa. 2.)

Re: [galaxy-dev] GTF files in Cufflinks and Tophat

2011-09-28 Thread Chorny, Ilya
Jeremy, 1.)Would you be interested in a feature in which the gtf files could be locally cached instead of only from history? 2.)Would you be interested in a feature in which cufflinks choses the genome in a fashion similar to how samtools know which which genome to use? i.e.:

[galaxy-dev] Additional eggs

2011-09-29 Thread Chorny, Ilya
Could you add PyX and Matplotlib(http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0.1/) to the eggs? They would be very useful for creating reports. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121

Re: [galaxy-dev] Python2.7 SAM to BAM Egg Not Fetchable

2011-09-30 Thread Chorny, Ilya
The egg is there, but the error still shows up. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Friday, September 30, 2011 6:40 AM To: Haden, Kirt Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re:

Re: [galaxy-dev] Python2.7 SAM to BAM Egg Not Fetchable

2011-09-30 Thread Chorny, Ilya
Same permissions as the 2.6 egg. -Original Message- From: Daniel Blankenberg [mailto:d...@bx.psu.edu] Sent: Friday, September 30, 2011 8:59 AM To: Chorny, Ilya Cc: Nate Coraor; Haden, Kirt; 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] Python2.7 SAM to BAM Egg Not Fetchable

Re: [galaxy-dev] Some changes to tophat and cufflinks wrappers for indexing loc files

2011-09-30 Thread Chorny, Ilya
I made some changes to the cufflinks and tophat wrapper to pull gtf files from an indexed loc file as opposed to from history. The diff's are attached. I made it an optional feature. Please let me know if this makes its way into galaxy-central. Best, Ilya Ilya Chorny Ph.D. Bioinformatics

Re: [galaxy-dev] Some changes to tophat and cufflinks wrappers for indexing loc files

2011-10-03 Thread Chorny, Ilya
Jeremy, Do you guys have an ETA for launching the data table changes? Thanks, Ilya From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Monday, October 03, 2011 5:41 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: Some changes to tophat and cufflinks wrappers

[galaxy-dev] strange history error

2011-10-11 Thread Chorny, Ilya
I am getting a strange error that I cannot figure out how to debug. It's from a second instance we have running on the same server. When I upload data it does not show me my history. I get the following messages from the log file. Thoughts? galaxy.web.framework DEBUG 2011-10-11 15:47:50,259

Re: [galaxy-dev] strange history error

2011-10-12 Thread Chorny, Ilya
Thanks, we actually had the wrong cookie_path set and that seemed to be causing the problem. Ilya -Original Message- From: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Sent: Wednesday, October 12, 2011 1:09 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] strange

[galaxy-dev] Trasfering Galaxy workflows to other instances

2011-10-12 Thread Chorny, Ilya
Is there a way of uploading workflows by saving the workflow to a file and copying the workflow files to a directory or editing a database file to point to them. When external authentication is invoked linking to workflows does not seem to work and copy and pasting from a file is very tedious.

Re: [galaxy-dev] Some changes to tophat and cufflinks wrappers for indexing loc files

2011-10-12 Thread Chorny, Ilya
attributes from a previous step as opposed to having to set them. From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Wednesday, October 12, 2011 1:22 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: Some changes to tophat and cufflinks wrappers for indexing loc files I made

Re: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper?

2011-10-16 Thread Chorny, Ilya
PDF report. Sent from my iPhone On Oct 15, 2011, at 7:36 PM, James Taylor ja...@jamestaylor.org wrote: Excerpts from Chorny, Ilya's message of 2011-10-14 23:46:25 +: Anyone know if it possible to pass the url (shown in the eye ball) to a tool wrapper? Ilya, this isn't currently

[galaxy-dev] Trouble getting setting dbkey of output data

2011-10-17 Thread Chorny, Ilya
I am having trouble setting the dbkey of an output data set. The input and output, respectively, is shown below. I copied this from the bowtie_wrapper.xml but the difference is that I do not have a condition on selecting the reference genome. My tool requires a .loc file. The tools completes

[galaxy-dev] attributes associted with xml inputs and outputs

2011-10-17 Thread Chorny, Ilya
Is there a list of associated attributes such as $input.ext, $input.dbkey and $input.id? Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.commailto:icho...@illumina.com Website:

Re: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper?

2011-10-17 Thread Chorny, Ilya
-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Sunday, October 16, 2011 7:36 AM To: James Taylor Cc: galaxy-dev Subject: Re: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper? PDF report. Sent from my iPhone On Oct 15, 2011, at 7:36 PM, James Taylor

Re: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper?

2011-10-17 Thread Chorny, Ilya
to the too wrapperl: -i input -i $input.dataset.id as well as --id_secret=$__app__.config.id_secret --cookie_path=$__app__.config.cookie_path -Original Message- From: Chorny, Ilya Sent: Monday, October 17, 2011 11:10 AM To: Chorny, Ilya; James Taylor Cc: galaxy-dev Subject: RE: [galaxy

Re: [galaxy-dev] Trouble getting setting dbkey of output data

2011-10-18 Thread Chorny, Ilya
Anybody, anybody? Thanks, Ilya From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Monday, October 17, 2011 9:31 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Trouble getting setting dbkey of output data I am

Re: [galaxy-dev] Trouble getting setting dbkey of output data

2011-10-18 Thread Chorny, Ilya
Great, thanks!!! From: Daniel Blankenberg [mailto:d...@bx.psu.edu] Sent: Tuesday, October 18, 2011 10:24 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Trouble getting setting dbkey of output data Hi Ilya, The 'actions' tagset must be within the ''data' tagset

[galaxy-dev] Re Acutal user code

2011-10-19 Thread Chorny, Ilya
Nate, I have been trying to figure out how to make the changes you suggested (i.e. write output files to the job_working_directory) and then move them over to files but I am having a difficult time navigating the code. If you could point me in the right direction, that would be helpful. I

[galaxy-dev] Upload File Button

2011-10-19 Thread Chorny, Ilya
I create an upload file button using upload.xml in one of my xml scripts. param name=file_data type=file size=30 label=File ajax-upload=true help=TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP

Re: [galaxy-dev] Upload File Button

2011-10-19 Thread Chorny, Ilya
I want to upload an experiment specific file from the workflow and bypass loading it into the history. -Original Message- From: James Taylor [mailto:ja...@jamestaylor.org] Sent: Wednesday, October 19, 2011 4:50 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy

[galaxy-dev] update of cufflinks and tophat to use dbkey attribute of input files

2011-10-20 Thread Chorny, Ilya
Hi Jeremy, I made some more modifications to the wrappers to allow for the tools to pull the genome information from the input files. The only drawback is that there is no way to validate whether the input has the dbkey attribute as a parameter (can you suggest a way to validate?). Attached

[galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?

2011-10-20 Thread Chorny, Ilya
I thought I would add this to the list in case anyone in the galaxy :) knew the answer. I get a mapping error every time I invoke url_for. What variable stores the base url for the galaxy instance? Thanks, Ilya -Original Message- From: Chorny, Ilya Sent: Wednesday, October 19, 2011

Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?

2011-10-20 Thread Chorny, Ilya
I get the following error from routes AttributeError: 'thread._local' object has no attribute 'mapper' -Original Message- From: James Taylor [mailto:ja...@jamestaylor.org] Sent: Thursday, October 20, 2011 5:46 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev

Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?

2011-10-21 Thread Chorny, Ilya
I need the base_url and the proxy. That is why I am using cookie_path. Any thoughts on how to get both. Thanks, Ilya -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Friday, October 21, 2011 6:11 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re

Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?

2011-10-21 Thread Chorny, Ilya
Also, I do not have access to trans in the Tools class in lib/galaxy/tools/__init__.py. Thanks, Ilya -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Friday, October 21, 2011 8:40 AM To: Greg Von

Re: [galaxy-dev] update of cufflinks and tophat to use dbkey attribute of input files

2011-10-21 Thread Chorny, Ilya
Can you guys show me an example of how this is used in the xml file? Thanks, Ilya From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Thursday, October 20, 2011 7:03 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: update of cufflinks and tophat to use dbkey attribute

Re: [galaxy-dev] Re Acutal user code

2011-10-21 Thread Chorny, Ilya
Sorry, the link was wrong. https://bitbucket.org/ichorny/galaxy-central-ilya2/ -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Friday, October 21, 2011 2:07 PM To: Nate Coraor (n...@bx.psu.edu) Cc

Re: [galaxy-dev] Re Acutal user code

2011-10-21 Thread Chorny, Ilya
. Probably should have done a merge first. I can redo it if you like. Let me know. Ilya -Original Message- From: Chorny, Ilya Sent: Friday, October 21, 2011 2:11 PM To: Chorny, Ilya; Nate Coraor (n...@bx.psu.edu) Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: Re Acutal user code Sorry, the link

Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?

2011-10-24 Thread Chorny, Ilya
- From: James Taylor [mailto:ja...@jamestaylor.org] Sent: Friday, October 21, 2011 9:47 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper? Excerpts from Chorny, Ilya's message of 2011-10-21

[galaxy-dev] Broad IGV

2011-10-24 Thread Chorny, Ilya
I saw some posts and a commit which allows one to use broad IGV within galaxy but I do not see a tool, a link, or an option. Can someone explain how to set that up? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work:

Re: [galaxy-dev] Re Acutal user code

2011-10-27 Thread Chorny, Ilya
Hi Nate, Any updates? Thanks, Ilya -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Friday, October 21, 2011 2:24 PM To: Nate Coraor (n...@bx.psu.edu) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re

Re: [galaxy-dev] Modifying the GATK wrappers to pick genome infomration from bam/sam dbkey attribute

2011-10-27 Thread Chorny, Ilya
Hi Dan, I want to modify the wrappers to get genome information from the bam/sam attribute. I did this for the tophat/cufflinks wrappers. I add another option to select genome called attribute and then I pass $bam.metadata.dkey in the command line (see example below). Is this something you

Re: [galaxy-dev] Modifying the GATK wrappers to pick genome infomration from bam/sam dbkey attribute

2011-10-27 Thread Chorny, Ilya
Blankenberg [mailto:d...@bx.psu.edu] Sent: Thursday, October 27, 2011 11:51 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: Modifying the GATK wrappers to pick genome infomration from bam/sam dbkey attribute Hi Ilya, You can validate dbkeys using validators including metadata

Re: [galaxy-dev] Re Acutal user code

2011-10-27 Thread Chorny, Ilya
Sweet!! Can't wait to see it. Thanks, Ilya -Original Message- From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu] Sent: Thursday, October 27, 2011 1:24 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: Re Acutal user code Yup, cleaning up some things that were

Re: [galaxy-dev] Clusters, Runners, and user credentials

2011-10-31 Thread Chorny, Ilya
Lyod, See Nate's email below Title: Actual user code. We have been working on implementing this feature in galaxy. The code is still in development but feel free to test it out and let us know how it works for you. Best, Ilya -Original Message- From:

Re: [galaxy-dev] Clusters, Runners, and user credentials

2011-10-31 Thread Chorny, Ilya
BTW, I am not sure if PBS works with drmaa. If not then the code will need to be ported to work with pbs. Ilya -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Monday, October 31, 2011 3:27 PM

Re: [galaxy-dev] Clusters, Runners, and user credentials

2011-10-31 Thread Chorny, Ilya
PM To: Chorny, Ilya Cc: Lloyd Brown; Galaxy Dev List Subject: Re: [galaxy-dev] Clusters, Runners, and user credentials Many of us are using the PBS job runner (for TORQUE) and would definitely be interested in a port. How do you deal with making sure the user's environment is configured

Re: [galaxy-dev] Re Acutal user code

2011-10-31 Thread Chorny, Ilya
PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: Re Acutal user code Chorny, Ilya wrote: Sweet!! Can't wait to see it. Have a look: https://bitbucket.org/natefoo/galaxy-central-ichorny/ Caveats: * job_working_directory has to be in a shared filesystem

[galaxy-dev] Looks like actual user breaks splitting

2011-11-02 Thread Chorny, Ilya
Hey John, Any thoughts? Ilya Traceback (most recent call last): File /home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/runners/tasks.py, line 73, in run_job tasks = splitter.do_split(job_wrapper) File /home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/splitters/multi.py, line 73,

Re: [galaxy-dev] Re Acutal user code

2011-11-02 Thread Chorny, Ilya
Everything seems to be working correctly, including splitting. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Wednesday, November 02, 2011 9:25 AM To: Nate Coraor (n...@bx.psu.edu) Cc: galaxy-dev

[galaxy-dev] Error when clicking on published workflows

2011-11-04 Thread Chorny, Ilya
URL: http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test Module paste.exceptions.errormiddleware:143 in __call__ http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya
be going on? If I comment out the move the upload works just fine. Thanks, Ilya -Original Message- From: Chorny, Ilya Sent: Friday, November 04, 2011 11:11 AM To: Chorny, Ilya; Nate Coraor (n...@bx.psu.edu); Duddy, John Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Looks like

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya
: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Friday, November 04, 2011 4:50 PM To: Nate Coraor (n...@bx.psu.edu) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Looks like actual user breaks splitting I am getting

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-07 Thread Chorny, Ilya
, 2011 7:57 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Looks like actual user breaks splitting On Nov 4, 2011, at 8:03 PM, Chorny, Ilya wrote: Looks like the mv is something I added and forgot about. I changed it to shutil.copyfile and it works fine. This also has

Re: [galaxy-dev] Error when clicking on published workflows

2011-11-07 Thread Chorny, Ilya
...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Friday, November 04, 2011 2:45 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Error when clicking on published workflows URL: http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test Module

[galaxy-dev] Workflow output selection bug

2011-11-07 Thread Chorny, Ilya
I think there is another bug in the output selection of the workflows. If I select only certain number of outputs (by selecting the orange star) to be show in history following a workflow and then edit the workflow to show more outputs, the number of outputs in the history does not change and

[galaxy-dev] Error in log

2011-11-10 Thread Chorny, Ilya
Our log is showing a strange error that does not seem to effect the way galaxy is behaving. Any thoughts? Thanks, Ilya f26d68045195cb8432494b6fbf HTTP/1.1 200 - - Python-urllib/2.6 galaxy.web.framework ERROR 2011-11-10 10:51:03,416 Uncaught exception in exposed API method: Traceback (most

[galaxy-dev] Actual User Code

2011-11-11 Thread Chorny, Ilya
When I try to link file paths into a shared data library from the admin menu it fails. I get the following in the log file: galaxy.jobs DEBUG 2011-11-11 13:24:38,280 (2645) Changing ownership of working directory with: /usr/bin/sudo -E /home/galaxy/production/Sept06/galaxy-central/sc

Re: [galaxy-dev] Actual User Code

2011-11-14 Thread Chorny, Ilya
) log.debug( finish(): Moved %s to %s % ( dataset_path.false_path, dataset_path.real_path ) ) From: Oren Livne [mailto:li...@uchicago.edu] Sent: Friday, November 11, 2011 1:33 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Actual User Code Check the permissions

[galaxy-dev] Grooming Error when linking bam files instead of copying into galaxy

2011-11-16 Thread Chorny, Ilya
The uploaded files need grooming, so change your Copy data into Galaxy? selection to be Copy files into Galaxy instead of Link to files without copying into Galaxy so grooming can be performed. Thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne

[galaxy-dev] Delete toolshed repository

2011-11-18 Thread Chorny, Ilya
I want to delete a test repository I created on http://toolshed.g2.bx.psu.edu/repository?webapp=community. Is that possible? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email:

Re: [galaxy-dev] PATH env variable for SGE jobs

2011-12-02 Thread Chorny, Ilya
Or you could create a directory in tool-deps called bowtie under bowtie create a default directory and in default create an env.sh file which set yours path correctly. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf