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 Is this instance using the run job as user patch, and if so, does the user running the job have permission to access the egg? Thanks for using Galaxy, Dan On Sep 30, 2011, at 11:36 AM, Chorny, Ilya wrote: > 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: [galaxy-dev] Python2.7 SAM to BAM Egg Not Fetchable > > Haden, Kirt wrote: >> Hi, >> >> >> >> When I run Galaxy under Python 2.7, I am unable to run SAM to BAM tools >> without getting the following error (below). The same configuration with >> Python 2.6 does not have an issue. The error seems to indicate bx_python >> eggs are not fetchable. What am I doing wrong? > > Hey Kirt, > > Are you running it on a machine with no Internet access? If not, can you run: > > python ./scripts/fetch_eggs.py > > With python set to your 2.7 version? > > Thanks, > --nate > >> >> >> >> Error report below: >> >> >> >> GALAXY TOOL ERROR REPORT >> >> ------------------------ >> >> >> >> This error report was sent from the Galaxy instance hosted on the server >> "ussd-dev-lnx01.illumina.com" >> >> --------------------------------------------------------------------- >> - >> ------- >> >> This is in reference to dataset id 301 from history id 68 >> >> --------------------------------------------------------------------- >> - >> ------- >> >> You should be able to view the history containing the related history >> item >> >> >> >> 7: SAM-to-BAM on data 6: converted BAM >> >> >> >> by logging in as a Galaxy admin user to the Galaxy instance referenced above >> and pointing your browser to the following link. >> >> >> >> ussd-dev-lnx01.illumina.com/history/view?id=42e99d98e0ee2844 >> >> --------------------------------------------------------------------- >> - >> ------- >> >> The user 'kha...@illumina.com' provided the following information: >> >> >> >> >> >> --------------------------------------------------------------------- >> - >> ------- >> >> job id: 200 >> >> tool id: sam_to_bam >> >> --------------------------------------------------------------------- >> - >> ------- >> >> job command line: >> >> python /home/galaxy/eval/sept09/galaxy-central/tools/samtools/sam_to_bam.py >> >> --input1=/home/galaxy/production/Sept06/galaxy-central/database/files/000/dataset_300.dat >> --dbkey=PhiX >> --output1=/home/galaxy/production/Sept06/galaxy-central/database/files/000/dataset_301.dat >> --index_dir=/home/galaxy/eval/sept09/galaxy-central/tool-data >> >> --------------------------------------------------------------------- >> - >> ------- >> >> job stderr: >> >> Traceback (most recent call last): >> >> File >> "/home/galaxy/eval/sept09/galaxy-central/tools/samtools/sam_to_bam.py", line >> 14, in ? >> >> import pkg_resources; pkg_resources.require( "bx-python" ) >> >> File >> "/home/galaxy/eval/sept09/galaxy-central/lib/galaxy/eggs/__init__.py" >> , >> line 415, in require >> >> raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) >> >> galaxy.eggs.EggNotFetchable: ['bx_python'] >> >> >> >> --------------------------------------------------------------------- >> - >> ------- >> >> job stdout: >> >> >> >> --------------------------------------------------------------------- >> - >> ------- >> >> job info: >> >> None >> >> --------------------------------------------------------------------- >> - >> ------- >> >> job traceback: >> >> None >> >> --------------------------------------------------------------------- >> - >> ------- >> >> (This is an automated message). >> >> >> Thanks, >> >> Kirt Haden >> Sr. Mgr. Engineering >> Illumina, Inc. >> 9885 Towne Centre Drive >> San Diego, CA 92121 >> Tel: 858.202.4655 >> Fax: 858.202.4545 >> Email: kha...@illumina.com<mailto:kha...@illumina.com> >> Website: www.illumina.com<http://www.illumina.com/> >> > >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this and other >> Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this and other Galaxy > lists, please use the interface at: > > http://lists.bx.psu.edu/ > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this and other > Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
