Hey Nate, Yes, I did run this as part of the setup and it looks like I have all the eggs: total 8071 -rw-r--r-- 1 galaxy aladdin 78031 Sep 22 08:14 amqplib-0.6.1-py2.6.egg -rw-r--r-- 1 galaxy aladdin 77872 Sep 27 12:10 amqplib-0.6.1-py2.7.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 22 08:14 Babel-0.9.4-py2.6.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 27 12:09 Babel-0.9.4-py2.7.egg drwxr-xr-x 4 galaxy aladdin 34 Sep 22 08:14 Beaker-1.4-py2.6.egg drwxr-xr-x 4 galaxy aladdin 34 Sep 27 12:10 Beaker-1.4-py2.7.egg drwxr-xr-x 5 galaxy aladdin 96 Sep 22 08:14 bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.6-linux-x86_64-ucs4.egg drwxr-xr-x 5 galaxy aladdin 96 Sep 27 12:09 bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.7-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 35 Sep 22 08:14 Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 35 Sep 27 12:09 Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg drwxr-xr-x 3 galaxy aladdin 63 Sep 22 11:36 decorator-3.1.2-py2.6.egg drwxr-xr-x 3 galaxy aladdin 63 Sep 27 12:11 decorator-3.1.2-py2.7.egg drwxr-xr-x 4 galaxy aladdin 73 Sep 23 11:09 docutils-0.7-py2.6.egg drwxr-xr-x 4 galaxy aladdin 73 Sep 27 12:11 docutils-0.7-py2.7.egg -rw-r--r-- 1 galaxy aladdin 34016 Sep 22 08:14 drmaa-0.4b3-py2.6.egg -rw-r--r-- 1 galaxy aladdin 33952 Sep 27 12:09 drmaa-0.4b3-py2.7.egg -rw-r--r-- 1 galaxy aladdin 51610 Sep 22 08:14 elementtree-1.2.6_20050316-py2.6.egg -rw-r--r-- 1 galaxy aladdin 51457 Sep 27 12:10 elementtree-1.2.6_20050316-py2.7.egg drwxr-xr-x 5 galaxy aladdin 52 Sep 22 08:14 GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.6.egg drwxr-xr-x 5 galaxy aladdin 52 Sep 27 12:10 GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.7.egg -rw-r--r-- 1 galaxy aladdin 7107 Sep 22 08:14 lrucache-0.2-py2.6.egg -rw-r--r-- 1 galaxy aladdin 7083 Sep 27 12:09 lrucache-0.2-py2.7.egg drwxr-xr-x 4 galaxy aladdin 32 Sep 22 08:13 Mako-0.4.1-py2.6.egg drwxr-xr-x 4 galaxy aladdin 32 Sep 27 12:09 Mako-0.4.1-py2.7.egg drwxr-xr-x 4 galaxy aladdin 38 Sep 22 08:14 MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 38 Sep 27 12:10 MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg -rw-r--r-- 1 galaxy aladdin 425930 Sep 22 08:14 MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg -rw-r--r-- 1 galaxy aladdin 425988 Sep 27 12:10 MySQL_python-1.2.3c1_5.1.41_static-py2.7-linux-x86_64-ucs4.egg drwxr-xr-x 5 galaxy aladdin 45 Sep 22 08:15 nose-0.11.1-py2.6.egg drwxr-xr-x 5 galaxy aladdin 45 Sep 27 12:10 nose-0.11.1-py2.7.egg -rw-r--r-- 1 galaxy aladdin 5724 Sep 22 08:14 NoseHTML-0.4.1-py2.6.egg -rw-r--r-- 1 galaxy aladdin 5718 Sep 27 12:09 NoseHTML-0.4.1-py2.7.egg -rw-r--r-- 1 galaxy aladdin 3744 Sep 22 08:14 NoseTestDiff-0.1-py2.6.egg -rw-r--r-- 1 galaxy aladdin 3740 Sep 27 12:10 NoseTestDiff-0.1-py2.7.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 22 08:14 numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 27 12:10 numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 22 08:15 Paste-1.6-py2.6.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 27 12:10 Paste-1.6-py2.7.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 22 08:14 PasteDeploy-1.3.3-py2.6.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 27 12:09 PasteDeploy-1.3.3-py2.7.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 22 08:15 PasteScript-1.7.3-py2.6.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 27 12:10 PasteScript-1.7.3-py2.7.egg -rw-r--r-- 1 galaxy aladdin 78539 Sep 22 08:14 pexpect-2.4-py2.6.egg -rw-r--r-- 1 galaxy aladdin 78460 Sep 27 12:09 pexpect-2.4-py2.7.egg drwxr-xr-x 4 galaxy aladdin 34 Sep 22 08:14 pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg -rw-r--r-- 1 galaxy aladdin 381997 Sep 27 12:10 pycrypto-2.0.1-py2.7-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 158 Sep 22 08:13 pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 158 Sep 27 12:09 pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 34 Sep 22 08:15 python_daemon-1.5.5-py2.6.egg drwxr-xr-x 4 galaxy aladdin 34 Sep 27 12:10 python_daemon-1.5.5-py2.7.egg -rw-r--r-- 1 galaxy aladdin 145984 Sep 22 08:14 python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg -rw-r--r-- 1 galaxy aladdin 146031 Sep 27 12:10 python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 34 Sep 22 08:14 Routes-1.12.3-py2.6.egg drwxr-xr-x 4 galaxy aladdin 34 Sep 27 12:10 Routes-1.12.3-py2.7.egg -rw-r--r-- 1 galaxy aladdin 113910 Sep 22 08:14 simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg -rw-r--r-- 1 galaxy aladdin 113704 Sep 27 12:10 simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg drwxr-xr-x 4 galaxy aladdin 38 Sep 22 08:14 SQLAlchemy-0.5.6_dev_r6498-py2.6.egg drwxr-xr-x 4 galaxy aladdin 38 Sep 27 12:10 SQLAlchemy-0.5.6_dev_r6498-py2.7.egg drwxr-xr-x 4 galaxy aladdin 35 Sep 22 08:15 sqlalchemy_migrate-0.5.4-py2.6.egg drwxr-xr-x 4 galaxy aladdin 35 Sep 27 12:09 sqlalchemy_migrate-0.5.4-py2.7.egg -rw-r--r-- 1 galaxy aladdin 64469 Sep 22 08:14 SVGFig-1.1.6-py2.6.egg -rw-r--r-- 1 galaxy aladdin 64713 Sep 27 12:10 SVGFig-1.1.6-py2.7.egg -rw-r--r-- 1 galaxy aladdin 21008 Sep 22 08:14 Tempita-0.1-py2.6.egg -rw-r--r-- 1 galaxy aladdin 20935 Sep 27 12:09 Tempita-0.1-py2.7.egg -rw-r--r-- 1 galaxy aladdin 0 Sep 30 07:37 tmp.txt drwxr-xr-x 4 galaxy aladdin 33 Sep 22 08:14 twill-0.9-py2.6.egg drwxr-xr-x 4 galaxy aladdin 33 Sep 27 12:10 twill-0.9-py2.7.egg -rw-r--r-- 1 galaxy aladdin 3982 Sep 22 08:14 wchartype-0.1-py2.6.egg -rw-r--r-- 1 galaxy aladdin 3978 Sep 27 12:10 wchartype-0.1-py2.7.egg drwxr-xr-x 4 galaxy aladdin 36 Sep 22 08:15 WebError-0.8a-py2.6.egg drwxr-xr-x 4 galaxy aladdin 36 Sep 27 12:10 WebError-0.8a-py2.7.egg drwxr-xr-x 4 galaxy aladdin 38 Sep 22 08:14 WebHelpers-0.2-py2.6.egg drwxr-xr-x 4 galaxy aladdin 38 Sep 27 12:09 WebHelpers-0.2-py2.7.egg -rw-r--r-- 1 galaxy aladdin 105194 Sep 22 08:15 WebOb-0.8.5-py2.6.egg -rw-r--r-- 1 galaxy aladdin 104720 Sep 27 12:09 WebOb-0.8.5-py2.7.egg -rw-r--r-- 1 galaxy aladdin 438487 Sep 22 08:14 Whoosh-0.3.18-py2.6.egg -rw-r--r-- 1 galaxy aladdin 436595 Sep 27 12:09 Whoosh-0.3.18-py2.7.egg -rw-r--r-- 1 galaxy aladdin 39776 Sep 22 08:15 wsgiref-0.1.2-py2.6.egg -rw-r--r-- 1 galaxy aladdin 39630 Sep 27 12:10 wsgiref-0.1.2-py2.7.egg Sam_to_Bam seems to be the only tool complaining. Thanks, Kirt -----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] 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 'khaden@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: khaden@illumina.com<mailto:khaden@illumina.com> Website: www.illumina.com<http://www.illumina.com/>
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