Re: [galaxy-dev] samtools dependency changes ?

2015-06-24 Thread Wolfgang Maier 
hmm, no replies yet, so is anybody able to reproduce this behavior and 
would you not consider it a bug?


Best,
Wolfgang


On 06/16/2015 03:11 PM, Wolfgang Maier wrote:

Dear all,

with older Galaxies (prior to latest_15.03 I think), you could satisfy
Galaxy's samtools dependence for indexing bam files by having a samtools
executable in tool-dependencies/samtools/default/bin (with the
tool-dependencies directory declared as tool_dependency_dir in
galaxy.ini of course).

Now (checked with latest_15.03 and .05), this is not working any more!
The executable will still be used during bam uploads, but not when a bam
file gets created by a tool.

The reason is that before the job runner (tested this with the local job
runner only) used to build the dependency shell command for dependency
'samtools' before finishing a job, but now the job wrapper finish method
fails because it naively expects to find samtools on $PATH.

Best,
Wolfgang

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[galaxy-dev] bowtie dataset pair input

2015-06-24 Thread Ryan G 
Hi all - It looks like bowtie's wrapper is working incorrectly for a list
of dataset pairs.  Its expecting all the forward reads in one dataset list
and the reverse reads in a separate dataset list.

Instead, I have a list of dataset pairs (for paired-end data).  This cannot
be provided to bowtie as input.  If I correct this, should I create a pull
request for it?  Alternatively, does someone already have a corrected
version of this?
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