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/183 de9d00131/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