[galaxy-dev] Problem finding depency for none toolshed tools

2015-07-01 Thread Christian Brenninkmeijer
Hi, I have been testing tools not yet ready for a tool-shed but had trouble finding the dependencies as there was no database entries to load these. The code in lib/galaxy/tools/deps/resolvers/galaxy_packages.py assumes that the env.sh or bin directory will be in dependency_dir/package/version

[galaxy-dev] running tophat2 on local Galaxy - can't find bowtie2

2015-07-01 Thread HARDING Simon
Hi I've set-up a local Galaxy instance and have been using the data manager / tool-shed to set up tools and indexes etc. I've installed both bowtie2 and tophat2 but when i come to run tophat 2 I get the following error: tophat2 --num-threads ${GALAXY_SLOTS:-4}

[galaxy-dev] Not seeing reference genome - Bowtie2

2015-07-01 Thread McCully, Dwayne (NIH/NIAMS) [C]
Hello Everyone, Performed a data retrieval using the rsync method for mm10 and also downloaded the .loc files per the Data Integration page to the tool-data directory. The paths match in the .loc file for bowtie2 of the mm10 download directory. My problem is that I'm not seeing mm10 in the

[galaxy-dev] cloudman launch

2015-07-01 Thread Alexander Vowinkel
Hi Enis, I am trying to launch my cloudman instance with this launcher again: https://launch.usegalaxy.org/launch You created the flavor for me because it wouldn't load my galaxyIndices from the snaps.yaml in my default bucket. I thought, this problem was fixed, but it still creates a