February 2012 - galaxy-dev - lists.galaxyproject.org

Apologies
by Ira Cooke 27 Feb '12

27 Feb '12

Dear List, Apologies for that last email. It seems my gmail account has somehow been compromised Please don't click on the link. Ira

1 0

Weird VDF format header
by thondeboer＠me.com 27 Feb '12

27 Feb '12

Hi, While technically not a Galaxy (Dev) question, but I am running into a non-standard VCF header in the GATK UnifiedGenotyper output. I see ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> Where Number=G and Number=A which does not pass the VCF Validator filter... Anyone know what is going on here? I had to change it to actual numbers (as the format describes..) Where does this header come from in the first place? Is it some standard header? Thanks Thon

1 0

Re: [galaxy-dev] Setting the output label based on input parameters?
by Ann Black-Ziegelbein 27 Feb '12

27 Feb '12

We are also "feeling the hurt" of not being able to carry the input dataset names through a complex workflow. We are also very interested in a solution similar to what Dave Walton has proposed,. Dave, would it be possible to receive a copy of your modified code? Does it work when there are multiple inputs? Ideally we would keep the names of datasets that are run through complex workflows the same as the workflow progresses. Sample mix-ups are a common scare, and with the current default naming it is not far fetched to see someone accidentally associating the end result with a different sample number. Thanks much, Ann

1 0

Upload file local option no longer appears
by James Vincent 27 Feb '12

27 Feb '12

Hello, I have been upload files to data libraries using the local file option to give a list of system file paths. Upon restarting galaxy (because of server reboot) I no longer have that option. The universe file has not changed and contains this, as it always has: # Add an option to the library upload form which allows administrators to # upload a directory of files. library_import_dir = /mnt/4TB When attempting to upload data sets to a library the only options in the pulldown are "Upload files" and "Import datasets from current history". I am logged in as the administrator. Am I missing something very obvious here? I can't seem to find what went wrong or changed. Thanks, Jim

2 1

Trouble linking to/displaying at local Genome Browser
by Josh Nielsen 27 Feb '12

27 Feb '12

Hello all, I am having some trouble getting a "display at" link to my local UCSC Genome Browser mirror to show up under my Galaxy jobs for viewing, although I can get the link to the online UCSC GB to display. I followed the suggestions in the following thread but it has yielded no results yet: http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td182929… . Here's what I have tried: - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file and duplicated the 'main' UCSC entry but changed the new entry's name to 'internalgb' and changed the URL to point to our local GB with * cgi-bin/hgTracks?* at the end - I set "*ucsc_display_sites = internalgb*" in universe_wsgi.ini - I made a modified copy of [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and created a tool link on the left side of the Galaxy page for it by adding it to the tool_conf.xml file (which works fine: when I click on it it loads our local Genome Browser inside the central Galaxy window frame) - I edited the HAIB_ucsc_tablebrowser.xml file according to the recommendation in the thread above: "*I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well*." So I gave it a unique id (changed ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field the same as the original/main UCSC tablebrowser (ucsc_table_direct1). Then I put the new HAIB id for our local tablebrowser into universe_wsgi.ini under the tool runners section as "*HAIB_table_direct1 = local:///*" - And of course I have restarted Galaxy after each change. Still after all of this I cannot see a "display at" link for bam & other files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to have "ucsc_display_sites = internalgb,main" set (for both browsers) the online/main GB will have a "display at" link on Galaxy jobs but no link shows for my local browser mirror. I'm also a little fuzzy on the relation between the ucsc_build_sites.txt file and the "*_ucsc_tablebrowser.xml" files (if any). Any tips as to what I might be missing here? Thanks! Josh

2 4

GATK metadata problems
by Curt Palm 27 Feb '12

27 Feb '12

When I try to run a GATK analysis that uses a bam file as input, I get the following error in the html page: Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue. when the input file is a bam file that has not run yet or is still running. So I can not set up multi step analysis or set up a work flow. I searched the mailing lists and could not find info on this, only a thread discussing wanting to use meta data from bam files to set the ref. genomes for GATK tools. is there a solution to this I am using the current version of Galaxy. thanks ******************************************************* Curtis J. Palm cpalm(a)stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994 cell: 408 858-7849 *******************************************************

2 1

Data not uploading in Local instance
by Jennifer Jackson 27 Feb '12

27 Feb '12

Hi Luciano, I am going to forward you question over the to galaxy-dev(a)bx.psu.edu mailing list where the development community will see and provide feedback to your question: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Best, Jen Galaxy team On 2/26/12 3:19 PM, Luciano Cosme wrote: > I have python 2.7 and it seems to be the problem with it. Just > formated the partition I had linux and fresh install everything and > still have same problem. I did what is recommended here too. > > > Check your Python version > > Galaxy's core functionality is compatible with *Python* versions *2.5*, > *2.6*, and *2.7*. (Version 2.4 support was last included in the November > 18, 2011 Distribution > <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2011_11_18#Python_Support>). > Before reporting bugs, please ensure that python --version reports one > of these three versions. If this is not the case, a simple solution is > to manipulate your shell's $PATH variable to place the correct version > first. This can be done for only Python by creating a new directory at > the front of $PATH and creating a symbolic link to python in that > directory: > > Toggle line numbers <http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy#> > > 1 <http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy#CA-78df7933c2e9e4b1411a7e60fd3…> % mkdir ~/galaxy-python > 2 <http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy#CA-78df7933c2e9e4b1411a7e60fd3…> % ln -s /path/to/python2.5 ~/galaxy-python/python > 3 <http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy#CA-78df7933c2e9e4b1411a7e60fd3…> %exportPATH=~/galaxy-python:$PATH > > > > > > On Sat, Feb 25, 2012 at 5:50 PM, Luciano Cosme <cosme.simple(a)gmail.com > <mailto:cosme.simple@gmail.com>> wrote: > > *Hi Everyone, > I have been running a Local Galaxy instance for a long time, but > now I am having some problems with uploading data. I am getting the > following error:* > > Can't create peek [Errno 2] No such file or directory:'/home/koala2/galaxy-dist/database/files/000/dataset_13.dat' > > > * > and from the Terminal:* > 127.0.0.1 - - [25/Feb/2012:17:45:00 -0500]"POST /library_common/library_item_updates HTTP/1.1" 200 -"http://127.0.0.1:8080/library_common/browse_library? > > > sort=name&operation=browse&f-description=All&f-name=All&f-deleted=False&cntrller=library_admin&async=false&show_item_checkboxes=false&webapp= > > > galaxy&id=f2db41e1fa331b3e&page=1" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" > > > > > * I reinstalled Unbutu and still having the same issue. I also removed Postgresql 9.1 and reinstalled it. I that it might be an issue with postgresql and not Galaxy, but I am not an expert. > Any suggestions will be appreciated. > > > Thank you. > > Luciano > * > > > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

1 0

Upload file script fails with OSError: [Errno 1]
by liram_vardi＠agilent.com 27 Feb '12

27 Feb '12

Hello, I would like to report on a Galaxy issue and the my proposed solution for it, hopefully it will be helpful to other Galaxy users that encounter [are encountering] the same problem. I tried to upload to my local Galaxy a file that I has been transferred by a FTP client. Then, when Galaxy tried to "pull out" this file from the FTP server, the operation failed with this traceback: File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 403, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 289, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 98, in convert_newlines shutil.move( temp_name, fname ) File "/usr/lib64/python2.6/shutil.py", line 260, in move copy2(src, real_dst) File "/usr/lib64/python2.6/shutil.py", line 96, in copy2 copystat(src, dst) File "/usr/lib64/python2.6/shutil.py", line 66, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/home/galaxy_upload/data_upload/...' The source file that I tried to copy had read/write permissions for all, therefore, logically, this operation should not have failed... I read a bit about this issue and I found out that python command shutil.move might raise an OSError when it tries to move a file to a partition where the user (galaxy in this case) has write permission but he is not the owner. More specifically, the exception fails to modify the copystat data. I have found a post suggesting to simply IGNORE this OSError that was raised from copystat... Therefore, I added the following "try" statement to "galaxy-dist/lib/galaxy/datatypes/sniff.py on line 98: try: shutil.move( temp_name, fname ) # Return number of lines in file. except OSError: pass return ( i + 1, None ) and it solved the problem completely! This is the link to the post that I took the solution from: http://bugs.python.org/issue1438480 I'm also attaching a modified "sniff.py". Hopefully, this will be helpful to other galaxy developers, Best, Liram

1 0

universe_wsgi.ini
by Brami, Daniel 27 Feb '12

27 Feb '12

I have been struggling with setting up my local Galaxy instance for the past two days. Can anyone post a copy of their universe_wsgi.ini file , with the sensitive info commented / removed? I need an instance that can handle local files greater than 2 GB (ie: does not go through POST method of browser to get data) and has permissions to use pre-built bowtie indices. Also, a FUNCTIONNAL copy of the 'bowtie_indices.loc' would be very helpful. (none of my prebuilt databases are appearing in drop down menu). Please assist. Daniel Brami Synthetic Genomics, Inc. Senior Research Associate, Bioinformatics 11149 North Torrey Pines Road La Jolla, California 92037 Phone: 858.433.2230 Fax: 858.754.2988 DBrami(a)SyntheticGenomics.com<mailto:DBrami@SyntheticGenomics.com> www.SyntheticGenomics.com<http://www.syntheticgenomics.com/>

2 3

How to get raw file name of the uploaded dataset
by Yingwei HU 26 Feb '12

26 Feb '12

Dear all, May I ask how to get the raw file name of the uploaded dataset? The value of $input assigned from <param name="input" type="data" format="xml"> is a file name like "dist-path/database/files/000/dataset_12.dat". However, I really need to get the raw file name like "abc.xml" which seems to be stored as attribute "name" of the uploaded dataset. How can I get the raw file name? Please help me. Thank you very much. Yingwei HU

2 2