Python2.7 SAM to BAM Egg Not Fetchable
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? 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/>
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/>
___________________________________________________________ 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:
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/>
___________________________________________________________ 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:
The egg is there, but the error still shows up. -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 '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/>
___________________________________________________________ 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:
___________________________________________________________ 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/
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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 '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/>
___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
Same permissions as the 2.6 egg. -----Original Message----- From: Daniel Blankenberg [mailto:dan@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 '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/>
___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
If this is running on a cluster, is there any chance the version of Python used on your cluster nodes was compiled with UCS-2 Unicode? You can check by running scripts/get_platforms.py on the host in question using the desired python binary. The eggs you have only work with UCS-4 Unicode. --nate Chorny, Ilya wrote:
Same permissions as the 2.6 egg.
-----Original Message----- From: Daniel Blankenberg [mailto:dan@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 '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/>
___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
Yes, this seem to be the issue. The Python on the compute nodes is not configured correctly. Thanks. Kirt -----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Friday, September 30, 2011 10:04 AM To: Chorny, Ilya Cc: Daniel Blankenberg; Haden, Kirt; 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] Python2.7 SAM to BAM Egg Not Fetchable If this is running on a cluster, is there any chance the version of Python used on your cluster nodes was compiled with UCS-2 Unicode? You can check by running scripts/get_platforms.py on the host in question using the desired python binary. The eggs you have only work with UCS-4 Unicode. --nate Chorny, Ilya wrote:
Same permissions as the 2.6 egg.
-----Original Message----- From: Daniel Blankenberg [mailto:dan@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 '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/>
___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
participants (4)
-
Chorny, Ilya -
Daniel Blankenberg -
Haden, Kirt -
Nate Coraor