Question: Need A Unix Script For The Galaxy Tool: Maf To Fasta (Version 1.0.1)
1
gravatar for JacobS
4.0 years ago by
JacobS850
West Lafayette
JacobS850 wrote:

Hi, I like the tool in Galaxy called MAF to FASTA (version 1.0.1), but want to incorporate it into an offline pipeline. Does anyone know how I can get a copy of this script?

Thanks!

maf galaxy • 2.5k views
ADD COMMENTlink modified 4.0 years ago by Pierre Lindenbaum102k • written 4.0 years ago by JacobS850

Galaxy is open source and so are tools (some might not). Main repo is here: https://bitbucket.org/galaxy/galaxy-central - tools are either there or in the Tool Shed - http://toolshed.g2.bx.psu.edu/

ADD REPLYlink written 4.0 years ago by martenson380
3
gravatar for Pierre Lindenbaum
4.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum102k wrote:

that one ?

https://github.com/thata/galaxy-dist/blob/master/tools/maf/interval_maf_to_merged_fasta.py

ADD COMMENTlink written 4.0 years ago by Pierre Lindenbaum102k

Almost, but your answer pointed me to the correct directory. Was looking for this one: https://github.com/thata/galaxy-dist/blob/master/tools/maf/maf_to_fasta_concat.py. Thanks!

ADD REPLYlink written 4.0 years ago by JacobS850

So, this python script is trying to access Galaxy dependencies: import sys from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) from bx.align import maf from galaxy.tools.util import maf_utilities. Anyway to get around this?

ADD REPLYlink written 4.0 years ago by JacobS850
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