Hi Ryan,
I have tried to collect a minimal set of dependencies you need to have
installed:
https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList
And we have a Galaxy Docker container that is working and should define
and test a fresh Galaxy installation:
https://github.com/bgruening/
I hate to hijack this thread, but I was thinking about this over the
holiday in how we are going to maintain a local up to date copy of Galaxy
ourselves. One thought would be to standardize on a single supported
platform aka an Amazon instance and make sure everything works on that
single platform
over to it.
Thanks to all for the help.
Mike
From: John Chilton [jmchil...@gmail.com]
Sent: Monday, January 05, 2015 10:25 AM
To: Waldron, Michael H
Cc: Martin Čech; Björn Grüning; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Problem using FastQC in Ga
Thanks :)
2015-01-05 16:45 GMT-02:00 Björn Grüning :
> Hi,
>
> why do you need biopython for FASTQC?
> You can install biopython from the ToolShed and can depend on it:
>
> https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_64
>
> Cheers,
> Bjoern
>
> Am 05.01.2015 um 19:01 schrieb
Hi,
why do you need biopython for FASTQC?
You can install biopython from the ToolShed and can depend on it:
https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_64
Cheers,
Bjoern
Am 05.01.2015 um 19:01 schrieb Alfredo Guilherme Silva Souza:
> Has anyone used the Biopython in Galaxy
Hey Alfredo,
You shouldn't have to mess with eggs for tools -- those are primarily
dependencies of the core framework itself. Do you have biopython installed
and available in the environment (PYTHONPATH) of whatever user jobs are run
as? That is, if you open a plain python shell as the galaxy us
Has anyone used the Biopython in Galaxy ?
*Traceback (most recent call last):*
* File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py", line
10, in *
*import Bio.PDB.PDBParser*
*ImportError: No module named Bio.PDB.PDBParser*
Researching I saw that I have to work with eggs in
e
>
>
> From: John Chilton [jmchil...@gmail.com]
> Sent: Monday, January 05, 2015 10:25 AM
> To: Waldron, Michael H
> Cc: Martin Čech; Björn Grüning; galaxy-...@bx.psu.edu
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
&g
one.
Mike
From: John Chilton [jmchil...@gmail.com]
Sent: Monday, January 05, 2015 10:25 AM
To: Waldron, Michael H
Cc: Martin Čech; Björn Grüning; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
This looks like a bug - but unf
',
> 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
> ('changeset_revisions', '0b201de108b9')],
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&a
e:
paste.recursive.include_app_iter:
paste.recursive.script_name: ''
paste.throw_errors: True
webob._parsed_query_vars: (MultiDict([('tool_shed_url',
'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'),
('changeset_
_
> From: Björn Grüning [bjoern.gruen...@gmail.com]
> Sent: Sunday, January 04, 2015 12:46 PM
> To: Waldron, Michael H; Björn Grüning; galaxy-...@bx.psu.edu
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Mike,
>
> it can happen that wrappers versions do not
pel Hill
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Sunday, January 04, 2015 12:46 PM
To: Waldron, Michael H; Björn Grüning; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
Hi Mike,
it can happen that wrappers versions do
3, 2015 6:42 AM
> To: Waldron, Michael H; galaxy-...@bx.psu.edu
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Michael,
>
> which version of the FASTQC wrapper are you running? Can you point us to
> the exact build and toolshed version?
>
> Thanks,
&g
omputing Center
University of North Carolina at Chapel Hill
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Saturday, January 03, 2015 6:42 AM
To: Waldron, Michael H; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
Hi
Hi Michael,
which version of the FASTQC wrapper are you running? Can you point us to
the exact build and toolshed version?
Thanks,
Bjoern
Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
> Having a problem with directing FastQC output in Galaxy. User is running a
> job whose command line look
Having a problem with directing FastQC output in Galaxy. User is running a job
whose command line looks like this:
# FastQC cl =
/nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
--outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files
/proj/galaxy/job_wo
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