[galaxy-dev] Problem finding depency for none toolshed tools

2015-07-01 Thread Christian Brenninkmeijer 
Hi,
I have been testing tools not yet ready for a tool-shed but had trouble finding 
the dependencies as there was no database entries to load these.


The code in lib/galaxy/tools/deps/resolvers/galaxy_packages.py assumes that the 
env.sh or bin directory will be in dependency_dir/package/version when in fact 
it is often in dependency_dir/
package/version/owner/package_name/revision.


I have created a pull request with some code to find the dependency in the sub 
directory

https://github.com/galaxyproject/galaxy/pull/413

As I am relatively new to galaxy I have probably broken lots of 
rules/agreements on how I did the pull request. If so please let me know where 
I went wrong so I can redo it properly.

Christian

PS.
This is my proposed change to 
lib/galaxy/tools/deps/resolvers/galaxy_packages.py:
def _find_dep_versioned( self, name, version, type='package', **kwds ):
#First try the way without owner/name/revision
path = join( self.base_path, name, version )
package = self._galaxy_package_dep(path, version)
if package != INDETERMINATE_DEPENDENCY:
return package
#now try with an owner/name/revision
for owner in listdir(path):
owner_path = path + / + owner
for package_name in listdir(owner_path):
if package_name.startswith(package_+name):
package_path = owner_path + / + package_name
for revision in listdir(package_path):
revision_path = package_path + / + revision
package = self._galaxy_package_dep(revision_path, 
version)
if package != INDETERMINATE_DEPENDENCY:
return package
return INDETERMINATE_DEPENDENCY

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[galaxy-dev] running tophat2 on local Galaxy - can't find bowtie2

2015-07-01 Thread HARDING Simon 
Hi 

I've set-up a local Galaxy instance and have been using the data manager / 
tool-shed to set up tools and indexes etc.

I've installed both bowtie2 and tophat2 but when i come to run tophat 2
I get the following error:

tophat2 --num-threads ${GALAXY_SLOTS:-4} 
/export/system0/home/galaxy/galaxy-dist/tool-data/mm9/bowtie2_index/mm9/mm9,/export/system0/home/galaxy/galaxy-dist/tool-data/mm9/bowtie2_index/mm9/mm9
 /export/system0/home/galaxy/galaxy-dist/database/files/000/dataset_14.dat

[2015-07-01 16:22:24] Beginning TopHat run (v2.0.9)
---
[2015-07-01 16:22:24] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.

Clearly there is an issue here with tophat2 knowing where bowtie2 is. What I 
can fathom is where this is assigned and how to get this working.

In my tool_dependency_dir/bowtie2 there are both 2.2.4 and 2.2.5 packages - 
this has confused me a bit, but i think it was because the 2.2.5 is a 
dependency of tophat2 and 2.2.4 a dependency of bowtie2.

Thanks in advance for any insight and help - I suspect it's something trivial 
as i'm quite new to Galaxy.
 
--
Simon D. Harding, PhD.
MRC HGU
MRC IGMM at University of Edinburgh
Crewe Road, EDINBURGH, EH4 2XU


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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[galaxy-dev] Not seeing reference genome - Bowtie2

2015-07-01 Thread McCully, Dwayne (NIH/NIAMS) [C] 
Hello Everyone,

Performed a data retrieval using the rsync method for mm10 and also downloaded 
the .loc files per the Data Integration page
to the tool-data directory.  The paths match in the .loc file for bowtie2 of 
the mm10 download directory.

My problem is that I'm not seeing mm10 in the Select Reference Genome from 
within Bowtie2.

Any tips would be appreciated

Dwayne
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[galaxy-dev] cloudman launch

2015-07-01 Thread Alexander Vowinkel 
Hi Enis,

I am trying to launch my cloudman instance with this launcher again:
https://launch.usegalaxy.org/launch

You created the flavor for me because it wouldn't load my
galaxyIndices from the snaps.yaml in my default bucket.

I thought, this problem was fixed, but it still creates a galaxyIndices
from the default snapshot (600GB) when using the Standard flavor.

When I use my flavor, it loads the snapshot, but it is a little outdated ;)

So my question: Is this behaviour expected? If no, are you going to
fix it soon? If not, could you update my flavor in the way that
galaxyIndices gets created from snap-6f0b211d ?

Further:
Should I update CM? I am still on the version from Jun 22.
I am still not sure what I need to change (my snaps.yaml) in order
to have my clean cluster creation still functioning.

Thanks,
Alexander
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