January 2012 - galaxy-user - lists.galaxyproject.org

Problem with <version_command> XML tag
by Greg Edwards 03 Jan '12

03 Jan '12

Hi, I'm in the process of adding a proteomics Perl script into a local copy of Galaxy. It seems like the version command in the galaxy/tools/myTools/myPerlTool.xml needs to have a full pathname. The doco indicates this should be enough: <version_command>myPerlTool -version</version_command>, and the few examples of it's use in galaxy/tools/*/*.xml are not full path, but on my installation this gives, in the Tool Version section of the View Details page of the run result /bin/sh: myPerlTool.pl: command not found I was expecting the version command to pick up the same path/environment as the main run. (Also, trivia dept, the doco in http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cversion_co… still references "<version_string>" instead of "<version_command>". I see from a search of source code commits this name change was made in July 2011. ) Thanks ! Greg E -- Greg Edwards gedwards2(a)gmail.com

2 1

Config info for: Problem with <version_command> XML tag
by Greg Edwards 03 Jan '12

03 Jan '12

Sorry folks, forgot the basics. It's a fresh install on Mac OS X 10.6.8 Started with sh run.sh in /Users/me/bio/galaxy Everything default. hg heads: changeset: 6298:b258de1e6cea tag: tip user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Nov 17 15:08:49 2011 -0500 summary: Pack js scripts. changeset: 6288:6483b3fbf1d6 branch: updates-for-tophat-1.3.1+ user: Jim Johnson <jj(a)umn.edu> date: Thu Nov 03 11:09:35 2011 -0500 summary: Tophat - fix typo in code. changeset: 6161:8d405036b501 branch: fastq-deinterlacer-memfix parent: 6160:70d41c4b591e parent: 6159:eafac82b3767 user: John Chilton <jmchilton(a)gmail.com> date: Mon Oct 24 15:36:24 2011 -0500 summary: Merging JJ fix with new branch Let me know if other config info is important -- Greg Edwards gedwards2(a)gmail.com

1 0

ftp upload
by Gabor Bartha 03 Jan '12

03 Jan '12

I have tried to use ftp to upload files to main.g2.bx.psu.edu but the jobs have been failing with: 421 service not available, remote server has closed connection after about 1.5GB. Isn't ftp the way you are supposed to upload large files? The file I am uploading is ~6GB in size. Gábor Bartha, Ph.D. Director of Information Sciences Synergenics, LLC 863 Mitten Rd., Suite 101 Burlingame, CA 94010 650-777-5202

2 1

problem upload data file
by Eric Guo 03 Jan '12

03 Jan '12

Hi everyone, I'd like to upload my sequencing data file, 36 GB, onto galaxy. My data is on a computer cluster in my institute. So I use ssh shell ftp commands to connect to galaxy and upload the data(ftp> put filename). And the connection appears to be fine as far as I can tell. I tried few times. Every time the uploading is fine in the beginning. However, when about 12 GB of my dataset is uploaded (according to Galaxy upload file page), the upload stops, and an error message pop up in the terminal on my Mac saying "a broken pipeline". I never had this problem before when I was using FTP programs like CyberDuck. Has anyone have similar problems using ssh command lines to upload data? What's the correct way to upload data from a computer cluster? Thanks in advance for your help. -Eric

2 1

Not able to get data from UCSC table browser
by Peng Yu 03 Jan '12

03 Jan '12

Hi, I'm trying to get data from UCSC table browser. However, the browser always show "Waiting for main.g2.bx.psu.edu...". Is there any problem with the galaxy server? -- Regards, Peng

4 3

tool_type="data_source_async"
by Matt Vincent 03 Jan '12

03 Jan '12

Hello all, I am trying to configure an Asynchronous tool (I can get it to work synchronously). My configuration looks something like this for the tool: <?xml version="1.0"?> <tool name="mytoolname" id="myunique_tool_id_1" tool_type="data_source_async"> <description>mytool description</description> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://myurl" check_values="false" method="post"> <display>Go to MyTool $GALAXY_URL</display> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> <request_param galaxy_name="URL" remote_name="URL" missing="" /> <request_param galaxy_name="jobname" remote_name="jobname" missing="N/A" /> </request_param_translation> <uihints minwidth="800"/> <outputs> <data name="output" format="zip" /> </outputs> <options sanitize="False" refresh="True"/> </tool> This works fine and downloads the data, but I was expecting Galaxy to post another GALAXY_URL parameter for me to generate the data and than post back to Galaxy once done. This is described here... http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources However, I never receive “another” GALAXY_URL as descripbed in Step 1 of the Asynchronous data depositing section. I am using the most recent version of Galaxy. Can someone please show an example? Matt

1 0