Hi Charles, I will try to fix that as soon as possible. Will get back to you. Bjoern
> Hi, > > > I' am running galaxy locally and I have installed Bismark and its > dependencies from the Galaxy main tool shed. I receive multiple errors > when using a small test dataset. > > > (1) My first error occurs when I try running Bismark bisulfite mapper > (bowtie2): > > > > > Error indexing reference sequence > /bin/sh: > /Users/charlesmurphy/Desktop/Research/tools/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark/183de9d00131/bismark/bismark_genome_preparation: > No such file or directory > > > > > Which I can fix by editing the env.sh file in the dependencies > directory. I change: > SCRIPT_PATH=/Users/charlesmurphy/Desktop/Research/tools/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark/183de9d00131/bismark; > > > To: > > SCRIPT_PATH=/Users/charlesmurphy/Desktop/Research/tools/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark/183de9d00131/bismark/bismark_wrapper; > > > > (2) My second error occurs when I try running Bismark methylation > extractor: > > > > > usage: bismark_methylation_extractor.py [-h] [--infile INFILE] > [--single-end] > > [--paired-end] > [--report-file REPORT_FILE] > [--comprehensive] [--merge-non-cpg] > [--no-overlap] [--compress COMPRESS] > [--ignore-bps IGNORE_BPS] > [--cpg_ot CPG_OT] [--chg_ot CHG_OT] > [--chh_ot CHH_OT] > [--cpg_ctot CPG_CTOT] > [--chg_ctot CHG_CTOT] > [--chh_ctot CHH_CTOT] > [--cpg_ob CPG_OB] > [--chg_ob CHG_OB] > [--chh_ob CHH_OB] > [--cpg_ctob CPG_CTOB] > [--chg_ctob CHG_CTOB] > [--chh_ctob CHH_CTOB] > [--cpg_context CPG_CONTEXT] > [--chg_context CHG_CONTEXT] > [--chh_context CHH_CONTEXT] > [--non_cpg_context NON_CPG_CONTEXT] > [--non_cpg_context_ot NON_CPG_CONTEXT_OT] > [--non_cpg_context_ctot NON_CPG_CONTEXT_CTOT] > [--non_cpg_context_ob NON_CPG_CONTEXT_OB] > [--non_cpg_context_ctob NON_CPG_CONTEXT_CTOB] > bismark_methylation_extractor.py: error: unrecognized arguments: > --bismark_path > /Users/charlesmurphy/Desktop/Research/tools/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark/183de9d00131/bismark > > > > > Seems to me the python wrapper lacks the code to tell galaxy where > the bismark_methylation_extractor executable is. I can go around the > error by editing bismark_methylation_extractor.py. I add the following > line: > parser.add_argument( '--bismark_path' ) > > > Then on line 72 I change: > cmd = 'bismark_methylation_extractor --no_header -o %s %s %s' > > > To: > > cmd = args.bismark_path + '/bismark_methylation_extractor --no_header > -o %s %s %s' > > > > > > I suspect I' am not doing something correctly. Let me know if anything > is unclear or if you need more information. Thanks for any help! > > > Charlie > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
