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:n...@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 '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"
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> Galaxy lists, please use the interface at:
> 
>   http://lists.bx.psu.edu/


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