I have a local galaxy instance on which I am trying to run Trinity. I have the following in my bashrc:
export TRINITY_HOME=/../../SOFTWARE/trinityrnaseq
I have tried to use this in three ways:
1) Included TRINITY_HOME in requirement type but this fails. I don't understand why, as Trinity is loaded in my environment
2) Included TRINITY_HOME in <tool_dependency>, changed the galaxy.ini file to include this: tool_dependency_dir=/../../SOFTWARE and made tool_dependencies.xml with TRINITY_HOME
3) As a last resort added this tag <tool_dependency> to trinityrnaseq.xml itself (this portion is commented out in the file below).
In all 3 situations I get the same error: command Trinity not found.
Kindly advice as to how I should proceed to resolve this issue?
trinityrnaseq.xml: [Edited to include the entire xml]
<tool id="trinityrnaseq" name="Trinity" version="0.0.1">
<!-- Written by Jeremy Goecks, now maintained here by bhaas -->
<description>De novo assembly of RNA-Seq data Using Trinity - Simple Interface</description>
<requirements>
<requirement type="set_environment">TRINITY_HOME</requirement>
</requirements>
<command>
\$TRINITY_HOME/Trinity --JM 1G --CPU 1 --full_cleanup --bflyHeapSpaceMax 5G
## Inputs.
#if str($inputs.paired_or_single) == "paired":
--left $inputs.left_input --right $inputs.right_input
#if $inputs.left_input.ext == 'fa':
--seqType fa
#else:
--seqType fq
#end if
#if str($inputs.library_type) != "None":
--SS_lib_type $inputs.library_type
#end if
--group_pairs_distance $inputs.group_pairs_distance
#else:
--single $inputs.input
#if str($inputs.input.ext) == 'fa':
--seqType fa
#else:
--seqType fq
#end if
#if str($inputs.library_type) != "None":
--SS_lib_type $inputs.library_type
#end if
#end if
## Additional parameters.
#if str($additional_params.use_additional) == "yes":
--min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph
#if $additional_params.bfly_opts != 'None':
--bfly_opts " $additional_params.bfly_opts "
#end if
#end if
## direct to output
> $trinity_log 2>&1
</command>
