[galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster

2011-11-03 Thread Carlos Borroto
Hi, I'm running into this error: Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_), When using SAM-to-BAM tool on a locally install Galaxy using a SGE cluster. I'm using the last version of galaxy-dist. I'm guessing I have a problem with the configuration for the tmp

Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster

2011-11-04 Thread Carlos Borroto
header output as a BWA option. Perhaps this will solve the immediate problem? Best, Jen Galaxy team On 11/3/11 12:43 PM, Carlos Borroto wrote: Hi, I'm running into this error: Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_), When using SAM-to-BAM tool

Re: [galaxy-dev] Installing Galaxy on local server

2011-11-08 Thread Carlos Borroto
Hi Toqa, I think you would want to use sh run.sh --daemon, so you don't have to keep the cli session open. To stop the daemon then you would use sh run.sh --stop-daemon. You could read much more about a production server installation at:

[galaxy-dev] Error working with workflows: KeyError: 'input_bam'

2011-11-08 Thread Carlos Borroto
Hi, I'm trying to develop a workflow using several tools from GATK and Picard sections among others. I'm able to run all the tools and from the history I'm creating a workflow, but I'm running into an error. I have copied the full debugging trace from my local Galaxy, I was able to import this

Re: [galaxy-dev] Error working with workflows: KeyError: 'input_bam'

2011-11-08 Thread Carlos Borroto
the reference value set before by another tool. Still I think there is a bug here. Thanks, Carlos On Tue, Nov 8, 2011 at 3:03 PM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi, I'm trying to develop a workflow using several tools from GATK and Picard sections among others. I'm able to run all

Re: [galaxy-dev] Error working with workflows: KeyError: 'input_bam'

2011-11-09 Thread Carlos Borroto
genome from your history. Thanks for using Galaxy, Dan On Nov 8, 2011, at 3:42 PM, Carlos Borroto wrote: I was able to make the error disappear. By trial and error I found the error appear when I set any tool with Using reference genome as To be set at runtime. But only for tools

Re: [galaxy-dev] Error working with workflows: KeyError: 'input_bam'

2011-11-09 Thread Carlos Borroto
/org_broadinstitute_sting_gatk_CommandLineGATK.html. Please let us know if we can provide additional information. Thanks for using Galaxy, Dan On Nov 9, 2011, at 11:01 AM, Carlos Borroto wrote: Hi Dan, Thanks for your response, but I'm still confused. When I edit the workflow there are two different kind

[galaxy-dev] Problem configuring local galaxy central installs and GATK beta pipeline

2011-11-15 Thread Carlos Borroto
Hi, I noted there have been a change on the way GATK tools read picard_index.loc, from tool_data_table_conf.xml: !-- Location of Picard dict files valid for GATK -- table name=gatk_picard_indexes comment_char=# columnsvalue, dbkey, name, path, tools_valid_for/columns file

Re: [galaxy-dev] Problem configuring local galaxy central installs and GATK beta pipeline

2011-11-15 Thread Carlos Borroto
. In the future the behavior will be properly enhanced to work properly on a comma separated listing. Thanks for using Galaxy, Dan On Nov 15, 2011, at 12:14 PM, Carlos Borroto wrote: Hi, I noted there have been a change on the way GATK tools read picard_index.loc, from

[galaxy-dev] ROD file for 'Unified Genotyper' only 'vcf'

2011-11-21 Thread Carlos Borroto
Hi, I found that the ROD file for the 'Unified Genotyper' tool, can be only vcf format. However for 'Count Covariates' and 'Indel Realigner', it can be vcf o, gatk_dbsnp or bed. Is this a bug or there is a limitation on GATK? Thanks, Carlos

[galaxy-dev] GATK / R local install configuration

2011-11-29 Thread Carlos Borroto
Hi, I'm testing the GATK pipeline and I ran into a problem with Variant Recalibrator tool. It seems I don't have correctly configure R and GATK on my instance, as this tool is failing with this error: mv: /Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat.pdf: No such

Re: [galaxy-dev] GATK / R local install configuration

2011-12-01 Thread Carlos Borroto
Hi, Any chances someone could give me hint on this issue? Thanks in advance, Carlos On Tue, Nov 29, 2011 at 2:02 PM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi, I'm testing the GATK pipeline and I ran into a problem with Variant Recalibrator tool. It seems I don't have correctly

Re: [galaxy-dev] [galaxy-user] Help need in troubleshooting cufflinks

2011-12-19 Thread Carlos Borroto
Hi Vijay, I ran into this error also, which by the way is not a galaxy issue but cufflinks and more specific is a Boost's bug. In my case it was caused because I was using the last version of Boost and there is a bug on that version causing the problem. You could apply this patch to boost:

[galaxy-dev] Empty files when importing with no copy from NFS source

2012-01-04 Thread Carlos Borroto
Hi, While trying to import some fastq files to a data library, using Upload directory of files and Link to files without copying into Galaxy, I end with empty datasets. My data files are accessed through NFS and I'm using the recommended option -noac: 10.2.90.89:/projects on /local/projects type

Re: [galaxy-dev] galaxy command line

2012-01-04 Thread Carlos Borroto
On Wed, Jan 4, 2012 at 2:25 PM, Ryan ngsbioinformat...@gmail.com wrote: On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad langho...@neb.com wrote: Usha: Galaxy is essentially a wrapper around other command line tools. So, while you could probably extract some of its pieces to run on the

Re: [galaxy-dev] Galaxy Server on Bio-Linux

2012-01-04 Thread Carlos Borroto
On Tue, Jan 3, 2012 at 11:36 AM, Nate Coraor n...@bx.psu.edu wrote: On Dec 20, 2011, at 1:09 PM, Bicak, Mesude wrote: Dear Galaxy Developers, We work in Professor Dawn Field's group (Molecular Evolution and Bioinformatics Research Group) at the NERC Environmental Bioinformatics Centre

Re: [galaxy-dev] Empty files when importing with no copy from NFS source

2012-01-04 Thread Carlos Borroto
On Wed, Jan 4, 2012 at 12:59 PM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi, While trying to import some fastq files to a data library, using Upload directory of files and Link to files without copying into Galaxy, I end with empty datasets. My data files are accessed through NFS

[galaxy-dev] Using workflows with steps with several inputs through the API

2012-01-05 Thread Carlos Borroto
Hi, Looking at workflow_execute.py, it seems to me there can be only one input for step, is this correct? or is there a wait to map more than one input and match them to an specific position in a particularly step? This is the workaround I found. I created 'Input Dataset' boxes for all of my

Re: [galaxy-dev] Galaxy Proxy by an External Apache Server

2012-01-05 Thread Carlos Borroto
On Thu, Jan 5, 2012 at 8:51 PM, Derrick LIN klin...@gmail.com wrote: Hi Carlos, You are right! I put the same config to site-available and now it works! Will do more testing/configuring base on that. Do you know why the location of the settings cause this issue? I would have to read a

Re: [galaxy-dev] Using workflows with steps with several inputs through the API

2012-01-09 Thread Carlos Borroto
On Mon, Jan 9, 2012 at 9:12 AM, Dannon Baker dannonba...@me.com wrote: Carlos, The method you describe below for mapping inputs is precisely the intended approach.  One reason for the long identifier being used instead of a simple step number is that step number (ordering as you would see

[galaxy-dev] How to set output name programmatically in workflows using the API?

2012-01-11 Thread Carlos Borroto
Hi, I would like to use the Rename Dataset action with a value base on the input. I was wondering if there is a way to do this programmatically? Searching the list I found this enhancement request that I think could help me, any update on this feature?

[galaxy-dev] How to use scripts/api/update.py?

2012-01-13 Thread Carlos Borroto
Hi, I'm trying to use the update.py script and is not clear for me what to use for 'url' in the usage line: usage: create.py key url [key=value ...]. Which I'm guessing is just a carry over from create.py. I tried passing the direct link to the dataset: $ ./update.py my_key

Re: [galaxy-dev] How to use scripts/api/update.py?

2012-01-17 Thread Carlos Borroto
None The dataset doesn't get updated. Is it possible to update datasets in a history? If so, how?. And, what I'm still doing wrong here causing the dataset in the library not to get updated? Thanks in advance for any help, Carlos On Fri, Jan 13, 2012 at 4:56 PM, Carlos Borroto carlos.borr

[galaxy-dev] Is it possible to pass runtime values to workflows through the API?

2012-01-18 Thread Carlos Borroto
Hi, I was wondering if is possible to pass runtime values to workflows thought the API? I want to run the same workflow for several inputs, but there are values other than the inputs that I need to change for each run. Is it possible to leave these values as 'To be set at runtime' and set them

Re: [galaxy-dev] Is it possible to pass runtime values to workflows through the API?

2012-01-18 Thread Carlos Borroto
Hi Dannon, On Wed, Jan 18, 2012 at 3:32 PM, Dannon Baker dannonba...@me.com wrote: On Jan 18, 2012, at 12:20 PM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi, I was wondering if is possible to pass runtime values to workflows thought the API? I want to run the same workflow for several

[galaxy-dev] How to manage stderr output from R?

2012-01-30 Thread Carlos Borroto
Hi all, I'm working on integrating cummeRbund[1] into Galaxy. This is a very helpful tool for analysis and visualization of cuffdiff output. My problem is any text output from running R code, puts the galaxy output in error state. Even if everything is working correctly and the outputs are

Re: [galaxy-dev] How to manage stderr output from R?

2012-01-30 Thread Carlos Borroto
if the tool fails. See the Cufflinks/compare/diff wrappers for examples of how this can be done. Good luck, J. On Jan 30, 2012, at 1:01 PM, Carlos Borroto wrote: Hi all, I'm working on integrating cummeRbund[1] into Galaxy. This is a very helpful tool for analysis and visualization

Re: [galaxy-dev] Problem previewing a tool in the Toolshed

2012-02-15 Thread Carlos Borroto
PM, Carlos Borroto wrote: Hi, I'm currently developing my first Galaxy tool. I'm working on a wrapper for R's library cummeRbund[1]. I got to the point where the tool although incomplete on functionality, I think is ready to be uploaded to the Toolshed. I was able to do so. I also made sure

Re: [galaxy-dev] Galaxy and Cluster options

2012-02-17 Thread Carlos Borroto
Hi Tanguy, L-A is correct in that you can set using the tool id different cluster options for different tools. For example I submit different tools to different queues: default_cluster_job_runner = drmaa://-q all.q -V/ upload1 = drmaa://-q short.q -V/ tophat = drmaa://-q long.q -V/ cufflinks =

Re: [galaxy-dev] Error 500 when trying to execute a workflow with the API

2012-02-21 Thread Carlos Borroto
Hi, Also, if it is in fact a history id and you will be using 'hda', remember to use 'hist_id=history_id' instead of 'Test API History'. -Carlos On Tue, Feb 21, 2012 at 6:46 PM, Dannon Baker dannonba...@me.com wrote: Hi Thon, You have the right idea about what's going wrong here.  Galaxy is

Re: [galaxy-dev] Error 500 when trying to execute a workflow with the API

2012-02-21 Thread Carlos Borroto
Hi Dannon, I think he is referring to the dataset input key in the dictionary. Thon, I think this thread could be helpful: http://galaxy-development-list-archive.2308389.n4.nabble.com/Using-workflows-with-steps-with-several-inputs-through-the-API-td4267374.html In summary, you want to ./display

Re: [galaxy-dev] Problem previewing a tool in the Toolshed

2012-02-29 Thread Carlos Borroto
. Thanks! Greg Von Kuster On Feb 15, 2012, at 2:24 PM, Carlos Borroto wrote: Hi Greg, Thanks for your answer. Would be great to get the tool to preview correctly but is not a big deal. I'm having a few more problems. I'm getting this error from time to time when I do hg push or even when I

Re: [galaxy-dev] Problem previewing a tool in the Toolshed

2012-02-29 Thread Carlos Borroto
your Galaxy instance or when you install your tool from the tool shed)?  If so, it should be displaying in the upload form.  What does your paster log say? On Feb 29, 2012, at 1:06 PM, Carlos Borroto wrote: Hi Greg, I did follow that link and I think the datatypes_conf.xml in the tool

Re: [galaxy-dev] Change Manage data Libraries

2012-03-14 Thread Carlos Borroto
On Wed, Mar 14, 2012 at 6:07 AM, Sivasangari NANDY nsi...@hotmail.com wrote: I've tried to write two times library_import_dir but it's not working, only the last directory is taken into account :                   library_import_dir = /sequences/fasta/maize/                  

Re: [galaxy-dev] [galaxy-user] How to Pass Parameter

2012-03-14 Thread Carlos Borroto
On Tue, Mar 13, 2012 at 2:15 PM, La Chi the_man.in...@yahoo.com wrote: hi galaxy developers , i have developed this parameter in xml file and i am passing  tl value to a function which is present in my python file , but when i select its type=text , it shows a text field with  tl , all i want

Re: [galaxy-dev] Change Manage data Libraries

2012-03-21 Thread Carlos Borroto
Yes. For example setting library_import_dir = /GALAXY_PATH/database/files/import, you would do something like: $ cd /GALAXY_PATH/database/files/import $ ln -s /sequences/fasta/maize $ ln -s /home/$USERNAME/blastdb_loc After this, you will have the option of selecting from maize or blastdb_loc

Re: [galaxy-dev] login not working on local instance

2012-03-22 Thread Carlos Borroto
In the past, every time I ran into this issue, cleaning browser's cookies fixed my problem. On Thu, Mar 22, 2012 at 11:50 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: Hi, For our fresh new local instance I created a user. But whenever I try to login it looks like I end up as

Re: [galaxy-dev] R scripts for DESeq

2012-03-26 Thread Carlos Borroto
Hi Vipin, I was wondering if there is any progress on getting your DESeq wrapper into the Tool Shed? I'm also highly interested on using DESeq inside Galaxy. Also, what you use for generating the read counts for DESeq? Do you produce these counts inside Galaxy? Thanks, Carlos On Thu, Feb 23,

Re: [galaxy-dev] R scripts for DESeq

2012-03-26 Thread Carlos Borroto
On 26 March 2012 14:01, Carlos Borroto carlos.borr...@gmail.com wrote: Hi Vipin, I was wondering if there is any progress on getting your DESeq wrapper into the Tool Shed? I'm also highly interested on using DESeq inside Galaxy. Also, what you use for generating the read counts for DESeq? Do

Re: [galaxy-dev] [galaxy-user] CummeRband in Galaxy platform

2012-03-30 Thread Carlos Borroto
Hi Bomba, I'm also quite interested on getting cummeRbund into Galaxy. I was able to start developing a tool to use it, but with tough time constraints at work and school, I haven't been able to get it to a point where I'm happy publishing it in the Main Toolshed. It is however in the Test

Re: [galaxy-dev] How does one survive the updates?

2012-04-25 Thread Carlos Borroto
On Wed, Apr 25, 2012 at 12:56 PM, Michael Moore michaelglennmo...@gmail.com wrote: My registration was gone.  My admin_user was overwritten.  I re-registered, and restored the file settings and restarted galaxy, but now no login sticks.  It does not complain about a registered user, but it does

[galaxy-dev] ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file

2012-04-27 Thread Carlos Borroto
It seems like GATK authors at Broad really really want you to phone home every time you use their software. I'm getting this error while running the lastest version: ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see

[galaxy-dev] Full path through API display.py

2012-05-01 Thread Carlos Borroto
Hi, Recently Full Path display was added as an option. I was wondering if this information could also be available when accessing a dataset information through the API. Thanks, Carlos ___ Please keep all replies on the list by using reply

Re: [galaxy-dev] Full path through API display.py

2012-05-02 Thread Carlos Borroto
overhead than help. On Tue, May 1, 2012 at 3:05 PM, Dannon Baker dannonba...@me.com wrote: Sure, good idea.  I'll tie it in. -Dannon On May 1, 2012, at 3:03 PM, Carlos Borroto wrote: Hi, Recently Full Path display was added as an option. I was wondering if this information could also

Re: [galaxy-dev] Full path through API display.py

2012-05-02 Thread Carlos Borroto
Done!. On Wed, May 2, 2012 at 4:35 PM, Dannon Baker dannonba...@me.com wrote: Yep, that's the right place to put it.  And you'll never hear me suggest someone *not* send in a pull request, so go for it :) -Dannon On May 2, 2012, at 3:08 PM, Carlos Borroto wrote: Thanks Dannon. I

[galaxy-dev] Keep header and output BAM options for NGS: SAM Tools/Filter SAM tool

2012-05-03 Thread Carlos Borroto
Hi, I regularly use NGS: SAM Tools/Filter SAM tool. Filtering after mapping with BWA is a required step. I feel my current approach to reintroduce the header after filtering is very wasteful. Wouldn't be great if this tool had an option to keep the header? This sounds simple enough. In fact

Re: [galaxy-dev] Running Galaxy behind apache2

2012-05-14 Thread Carlos Borroto
On Thu, May 10, 2012 at 4:23 PM, CHEBBI Mohamed Amine chebbimam...@gmail.com wrote: I configured the apache2.conf like above : If you are using Ubuntu or Debian, the place to put this configuration is '/etc/apache2/sites-available/default' not /etc/apache2/apache2.conf. Hope it helps, Carlos

Re: [galaxy-dev] How must I configure Apache ?

2012-05-18 Thread Carlos Borroto
Hi Julie, Could you answer a couple of questions? First, are you interested on integrating Galaxy with a third party authentication system? Second, do you expect heavy usage(I would say hundreds of concurrent users) where you would need several Galaxy servers with the work load balanced amount

Re: [galaxy-dev] How must I configure Apache ?

2012-05-24 Thread Carlos Borroto
the proxy balancer lines like this (it is in the hope to increase performances): Proxy balancer://galaxy Balancer member... ... /Proxy must I add in default file (and before or after the rewrite rules?) or in an other file ? Thank you in advance. Julie 2012/5/18 Carlos Borroto carlos.borr

Re: [galaxy-dev] Few questions about first time out with local install

2012-06-21 Thread Carlos Borroto
On Thu, Jun 21, 2012 at 8:54 AM, Alan V. Cowles alan.cow...@duke.edu wrote: My first question: Is there a way to make the galaxy server retrieve data from a local storage set, instead of uploading newly through the web interface? Http seems like an awfully inefficient way to transmit sequence

Re: [galaxy-dev] Fwd: Re: [galaxy-user] Linking to Compressed Data

2012-08-21 Thread Carlos Borroto
are uploaded. beware: it only supports one data set per zipped file - so gzipped fastqs are find.. but a tarball of a bunch of fastqs is not. Brad On Aug 21, 2012, at 10:23 AM, Carlos Borroto carlos.borr...@gmail.com wrote: Interesting... Hans, could you specify what tools currently available

Re: [galaxy-dev] The blastdb_p.loc sample is wrong.

2012-10-08 Thread Carlos Borroto
On Sun, Oct 7, 2012 at 3:02 PM, Shane Sturrock sh...@biomatters.com wrote: using xemacs, just the terminal based one. And typing a raw tab involves a tedious control sequence... there probably is an easier way, but I don't edit these loc files very often. Just hit 'Tab' in vi. Somehow I

Re: [galaxy-dev] Composite datatype output for Cuffdiff

2012-10-12 Thread Carlos Borroto
On Thu, Oct 11, 2012 at 6:14 PM, Jim Johnson johns...@umn.edu wrote: Checking to see if there is any interest in including a parameter option to select outputs for cuffdiff, potentially including a composite output and a cummeRbund sqlite database. Hi JJ, I'm highly interested in something

Re: [galaxy-dev] Anybody knows how to disable daily digest for this email list?

2012-10-15 Thread Carlos Borroto
On Mon, Oct 15, 2012 at 5:12 AM, Joachim Jacob joachim.ja...@vib.be wrote: I really could not find this. Anybody willing to show me? :-) Sure, go here: http://lists.bx.psu.edu/options/galaxy-dev After entering your credentials, Set Digest Mode is the second option from the top. Hope it helps,

Re: [galaxy-dev] How to get a shedtool to run locally

2012-10-17 Thread Carlos Borroto
On Mon, Oct 15, 2012 at 11:49 AM, Liisa Koski liisa.ko...@basf.com wrote: Hello, I've installed a tool to my local Galaxy installation via my local ToolShed. I would like to run this tool locally, and not have it submitted to the grid. I have tried two ids in the universe_wsgi.ini

Re: [galaxy-dev] How to get a shedtool to run locally

2012-10-19 Thread Carlos Borroto
On Fri, Oct 19, 2012 at 12:00 AM, Fields, Christopher J cjfie...@illinois.edu wrote: My local one is set up like this and it works (for augustus): toolshed.g2.bx.psu.edu/repos/bjoern-gruening/augustus/augustus/0.1 = pbs:///default/-l ncpus=1,mem=8gb,walltime=24:00:00/ The above is the

Re: [galaxy-dev] which .loc file for SAM to BAM?

2012-10-31 Thread Carlos Borroto
On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try SAM to BAM for a BAM file that has hg18 set as build I get a message that Sequences are not currently

Re: [galaxy-dev] which .loc file for SAM to BAM?

2012-11-01 Thread Carlos Borroto
, thank you for the pointer. I was only looking at this wiki page: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration Maybe this should point to your page? regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk andreas.kuntz...@mdc

[galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

2012-11-01 Thread Carlos Borroto
Hi, I've been researching the possibility of using dynamic job runner in combination with job splitting for blast jobs. My main interest is to create a rule where both the size of the query and the database are taken into consideration in order to select DRMAA and splitting options. My first

Re: [galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

2012-11-02 Thread Carlos Borroto
Hi Alex, On Fri, Nov 2, 2012 at 9:53 AM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: The dynamic runner is alive and well thanks to the continuous work of the author John Chilton and others. For instance, yesterday John committed code to galaxy-central that propagates tracebacks from the

Re: [galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

2012-11-02 Thread Carlos Borroto
On Fri, Nov 2, 2012 at 3:58 PM, Carlos Borroto carlos.borr...@gmail.com wrote: On Fri, Nov 2, 2012 at 9:53 AM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: The dynamic runner is alive and well thanks to the continuous work of the author John Chilton and others. For instance, yesterday John

Re: [galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

2012-11-05 Thread Carlos Borroto
On Fri, Nov 2, 2012 at 6:03 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: Here is the blastn rule procedure code and the relevant snippet of the default runner procedure. I just added the database based multiplier, so this part is very simple at the moment. I just set a bogus multiplier of

[galaxy-dev] Uncaught exception queueing job

2012-11-16 Thread Carlos Borroto
Hi all, I ran into this error while uploading a ~300mb file. I'm using latest galaxy-dist, Apache proxy and Torque/Maui throught DRMAA. After this error appear in the log, the dataset stays in grey. If I restart the galaxy daemon, the job gets correctly submitted. galaxy.jobs.runners.drmaa ERROR

Re: [galaxy-dev] Uncaught exception queueing job

2012-11-19 Thread Carlos Borroto
I want to add that this issue doesn't show up if I turn off 'use_tasked_jobs' for jobs splitting. I realize this feature is marked as not ready for production. I will stay away from it for the time being. Thanks, Carlos On Fri, Nov 16, 2012 at 5:13 PM, Carlos Borroto carlos.borr...@gmail.com

Re: [galaxy-dev] Uncaught exception queueing job

2012-11-19 Thread Carlos Borroto
I would like to recall the previous email. The error does happen even with 'use_tasked_jobs' set to false. It looks like I have some issues with my local torque install that I need to resolve. Thanks and sorry, Carlos On Mon, Nov 19, 2012 at 11:23 AM, Carlos Borroto carlos.borr...@gmail.com

Re: [galaxy-dev] Problem with Active Directory/LDAP authentication

2012-11-27 Thread Carlos Borroto
Hi Harris, I can't pin-point your issue exactly, to be honest I don't quite remember how I got to this working configuration. Still please take a look at this configuration as I'm using it in almost exactly the same enviroment, Centos 6/Apache 2.2.15/Active Directory... VirtualHost *:80

[galaxy-dev] Issue when enabling use_tasked_jobs with torque and nfs

2012-11-30 Thread Carlos Borroto
Hi, In my environment when I activate 'use_tasked_jobs' I'm getting this message in Info with ncbi_blast wrappers: /local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0: Job output not returned from cluster Still the dataset with the blast result is green and contains

Re: [galaxy-dev] add new slurm-drmaa runner to galaxy-central

2012-12-10 Thread Carlos Borroto
On Sat, Jul 21, 2012 at 6:12 AM, Di Pe dip...@gmail.com wrote: may be some other people would find this a useful enhancement: https://bitbucket.org/galaxy/galaxy-central/issue/778/add-new-slurm-drmaa-runner-to-galaxy Hi Di, I've been testing several grid scheduling software trying to find

Re: [galaxy-dev] Galaxy with Univa Grid Engine (UGE) instead of SGE?

2013-01-17 Thread Carlos Borroto
On Wed, Jan 16, 2013 at 7:28 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Renaming the file to replace the colon with (say) an underscore allows a manual qsub to work fine with UGE. I've edited Galaxy to avoid the colons (patch below) but the submission still fails. Hi Peter, After seeing

[galaxy-dev] Colon in drmout and drmerr file names creates issues with Torque and DRMAA when using 'use_tasked_jobs'.

2013-01-18 Thread Carlos Borroto
Hi All, Thanks to this email[1] from Peter Cock I was able to find what was causing the error I initially described here[2]. I also now have a theory of why this is happening. My unconfirmed guess. When a colon is present in the standard output or standard error file, someone betweent Galaxy,

Re: [galaxy-dev] Galaxy with Univa Grid Engine (UGE) instead of SGE?

2013-01-25 Thread Carlos Borroto
On Thu, Jan 24, 2013 at 11:04 AM, Dannon Baker dannonba...@me.com wrote: Hey Peter, Carlos, Thanks for tracking this down, I've updated the composite job/task id tag to use an underscore instead in changeset 8658:c901bbb4eca8. Hi Dannon, Thanks for the quick fix. I applied this fix

[galaxy-dev] Only custom genomes for uploads in data libraries

2013-01-25 Thread Carlos Borroto
Hi, I'm running latest galaxy-dist locally. When I try to upload a dataset to a data library through Admin, I only get the two custom genomes I have created for visualizations. If I use the regular upload tool under Get data, I do get to choose any of the genomes in:

[galaxy-dev] Tool shed and tools with dynamically generated select list parameters

2013-01-28 Thread Carlos Borroto
Hi, I'm trying to get lastz to show a locally cached reference. As I'm used to do I went ahead and copy tool-data/lastz_seqs.loc.sample(still included with galaxy-dist) to tool-data/lastz_seqs.loc and added my local references. Nothing happened. I get: galaxy.tools.parameters.dynamic_options

Re: [galaxy-dev] Tool shed and tools with dynamically generated select list parameters

2013-01-28 Thread Carlos Borroto
On Mon, Jan 28, 2013 at 5:29 PM, Greg Von Kuster g...@bx.psu.edu wrote: And that did the trick. Is this the expected way of handling these cases?. Yes, however, if your install the repository from the Galaxy administrator interface, this should all happen automatically for you. If you

Re: [galaxy-dev] Only custom genomes for uploads in data libraries

2013-01-29 Thread Carlos Borroto
On Mon, Jan 28, 2013 at 10:40 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Sun, Jan 27, 2013 at 10:04 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote: Actually, there an easier way to fix this without patching your Galaxy installation. Builds will show up in the library dbkey box

[galaxy-dev] Wiki reset password's email never arrives

2013-01-30 Thread Carlos Borroto
Hi, I need help recovering my Galaxy Wiki password. I enter my information and I get the message about my account existing and an email was sent, but I never receive this email. Thanks, Carlos ___ Please keep all replies on the list by

Re: [galaxy-dev] FW: install reference genome Bwa and Bowtie!

2013-01-31 Thread Carlos Borroto
On Thu, Jan 31, 2013 at 9:09 AM, Hakeem Almabrazi halmabr...@idtdna.com wrote: I was sure that was not the case (all in tabs). Here is my bwa_indices.loc file look like # #bwaReference /usr/local/galaxy_data/hg19/bwa/ hg19_reference_genome

[galaxy-dev] Local toolshed not working HTTPError: HTTP Error 400: Bad Request

2013-02-04 Thread Carlos Borroto
Hi, I interested in hosting a local toolshed. I was able to install it and add a tool to it. I have configured my local galaxy instance to pull tools from this local toolshed. As far as I can tell everything is working in the toolshed side of things, but when I try to install the tool I added I

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-02-04 Thread Carlos Borroto
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as your email' in the

Re: [galaxy-dev] Local toolshed not working HTTPError: HTTP Error 400: Bad Request

2013-02-04 Thread Carlos Borroto
On Mon, Feb 4, 2013 at 2:01 PM, Carlos Borroto carlos.borr...@gmail.com wrote: I can manually confirm this URL is incorrect: tool_shed_url=http://toolsheddev.bfx.brel.local:9009/repository_ids=ee9b707789bf4714changeset_revisions=71b062907e0d When I try to directly access it I get this error

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-02-04 Thread Carlos Borroto
On Mon, Feb 4, 2013 at 4:46 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard carlfeberh...@gmail.com wrote: Just to be clear, Dan - this solved the login issue and not the upload issue (in which case I'd owe Carlos a six-pack), correct? Sorry...this

Re: [galaxy-dev] Local toolshed not working HTTPError: HTTP Error 400: Bad Request

2013-02-04 Thread Carlos Borroto
Solved! It was related to my proxy configuration after all. Setting the no_proxy environment variable fixed this issue for me. I see this is a corner case but just in case someone else runs into it, this is a summary of what I did. If your network uses a http proxy who do not answer to local

Re: [galaxy-dev] Error with local toolshed and remote user authentication: HTTPError: HTTP Error 401: Authorization Required

2013-02-13 Thread Carlos Borroto
On Wed, Feb 13, 2013 at 10:38 AM, Nate Coraor n...@bx.psu.edu wrote: You'll need something here like: Satisfy Any Order deny,allow Deny from all Allow from your.galaxy.server Thanks Nate!, this worked flawlessly. My work around was to point galaxy to the toolshed paster

Re: [galaxy-dev] Error with local toolshed and remote user authentication: HTTPError: HTTP Error 401: Authorization Required

2013-02-13 Thread Carlos Borroto
On Wed, Feb 13, 2013 at 2:11 PM, Carlos Borroto carlos.borr...@gmail.com wrote: On Wed, Feb 13, 2013 at 10:38 AM, Nate Coraor n...@bx.psu.edu wrote: You'll need something here like: Satisfy Any Order deny,allow Deny from all Allow from your.galaxy.server Thanks Nate

Re: [galaxy-dev] Error with local toolshed and remote user authentication: HTTPError: HTTP Error 401: Authorization Required

2013-02-13 Thread Carlos Borroto
On Wed, Feb 13, 2013 at 3:10 PM, Greg Von Kuster g...@bx.psu.edu wrote: Carlos, Sorry you're having difficulty here. I'm not able to help very much here because I'm not familiar with the Galaxy remote user authentication process and I don't have an environment in which to mess with it.

Re: [galaxy-dev] Error with local toolshed and remote user authentication: HTTPError: HTTP Error 401: Authorization Required

2013-02-14 Thread Carlos Borroto
On Thu, Feb 14, 2013 at 10:30 AM, Nate Coraor n...@bx.psu.edu wrote: You may be able to get this to work by setting 'display_servers = galaxy_server_hostname' in your community_wsgi.ini file. This instructs Galaxy's remote user middleware to allow connections from this host even if a

Re: [galaxy-dev] New release : display problem

2013-02-14 Thread Carlos Borroto
On Thu, Feb 14, 2013 at 11:01 AM, Dannon Baker dannon.ba...@gmail.com wrote: Could you share with me a file that reproduces this behavior? I'm unable to do so on a fresh -dist clone after trying various files and file types. Do you see any errors in the console or galaxy log when this

Re: [galaxy-dev] New release : display problem

2013-02-15 Thread Carlos Borroto
On Fri, Feb 15, 2013 at 11:08 AM, Dannon Baker dannon.ba...@gmail.com wrote: Well, (un)fortunately this file works for me in both firefox and chrome on the current galaxy-dist. Just to confirm -- when you click the eye, it doesn't download the file either, right -- nothing at all happens?

Re: [galaxy-dev] New release : display problem

2013-02-21 Thread Carlos Borroto
: null, file_size: 969, model_class: HistoryDatasetAssociation, metadata_column_types: [int, str, str, int], id: 9664, misc_info: uploaded tabular file, metadata_dbkey: ?} ); Regards, Cyril On 02/15/2013 07:09 PM, Carlos Borroto wrote: On Fri, Feb 15, 2013 at 11:08 AM, Dannon

Re: [galaxy-dev] Tabular file metadata - columns names

2013-02-21 Thread Carlos Borroto
On Wed, Feb 20, 2013 at 9:57 AM, Peter Cock p.j.a.c...@googlemail.com wrote: [*] This is one reason why I've just switched the default BLAST+ output from the standard 12 column output to the extended 24 column output in v0.0.17 of the wrappers:

Re: [galaxy-dev] Installing Galaxy on ARM Architecture

2013-02-22 Thread Carlos Borroto
Hi Shun, Would you please share which third-party tools you are able to compile on ARM? I'll be very interested in knowing about that. I'm thinking on things like samtools, bowtie, tophat, cufflinks, bwa, ncbi_blast, etc. Thanks, Carlos On Fri, Feb 22, 2013 at 10:51 AM, Shun Liang

Re: [galaxy-dev] registration problem

2013-03-11 Thread Carlos Borroto
On Mon, Mar 11, 2013 at 9:04 AM, Wesley Schaal wesley.sch...@orgfarm.uu.se wrote: When trying to register a new user (which will be the administrator), the registration page declare success (Now logged in as foo) but I am still just an anonymous user. If I try to login, it appears to succeed

Re: [galaxy-dev] Configuring the time of permanently deleting data sets.

2013-07-09 Thread Carlos Borroto
Hi Ricardo, You might want to take a look at this[1] page in the wiki. The short answer is there is no way to configure purging datasets in Galaxy itself. It would be nice to do so. Galaxy does provide an external script that can be easily put in a cron job to do this. The script is

Re: [galaxy-dev] Setting torque queues

2013-08-14 Thread Carlos Borroto
On Tue, Apr 30, 2013 at 9:46 AM, Scott Hazelhurst scott.hazelhu...@wits.ac.za wrote: Below that is the output I get in the log. From the torque log it complains that there is no default queue specified. Hi Scott, Today I was hit by what it seems the same issue. In my case it was an issue with

[galaxy-dev] 'galaxy-api-tools' project

2013-08-26 Thread Carlos Borroto
Hi, I'm interested in developing a tool that would allow easy interaction with the Galaxy API. I started coding and this[1] is what I have so far. [1]https://github.com/cjav/galaxy-api-tools This is a pure release early, release often kind of project. In the current state many of the project's

Re: [galaxy-dev] Updating Galaxy Instance

2013-09-03 Thread Carlos Borroto
Hi Richard, After updating the code if you try to run the app, it will tell you if the database needs to be updated and how to do it. I don't know if there is a method to know if the database have been updated before updating the code. Hope it helps, --Carlos On Tue, Aug 27, 2013 at 11:59 AM,

[galaxy-dev] Looking for brave testers. New barcode splitter outputing splitted datasets directly to the history.

2013-09-06 Thread Carlos Borroto
Hi, I was wondering if I could get someone to test this new barcode splitter I wrote. The main reason for me to duplicate the already great fastx-toolkit based splitter, is so I can use galaxy's multiple output capabilities. You can find this tool in the testtoolshed for now(after some more

Re: [galaxy-dev] Looking for brave testers. New barcode splitter outputing splitted datasets directly to the history.

2013-09-10 Thread Carlos Borroto
. Best, Jen Galaxy team On Sep 10, 2013, at 11:49 AM, Carlos Borroto carlos.borr...@gmail.com wrote: Cool, I got a tweet about this tool from @GalaxyProject[1]. To further explain what I'm trying to accomplish here, as I realized not everybody might know what using Multiple Output Files

Re: [galaxy-dev] Looking for brave testers. New barcode splitter outputing splitted datasets directly to the history.

2013-09-10 Thread Carlos Borroto
://twitter.com/galaxyproject/status/377497531745595392 [2]http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run Best, Carlos On Fri, Sep 6, 2013 at 1:58 PM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi, I was wondering

[galaxy-dev] Proper way of using bioblend.galaxy.workflows.run_workflow() {'input': {'id': encoded dataset ID, 'src': '[ldda, ld, hda]'}

2013-09-11 Thread Carlos Borroto
Hi, I'm rewriting my galaxy-api-tools project to use bioblend. I can't believe I missed it the first time around. I'm a little confused reading about LibraryDatasetDatasetAssociation (ldda), LibraryDataset (ld) and HistoryDatasetAssociation (hda). I found something in the wiki[1] but is not

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