[galaxy-dev] package_bowtie_2_2_6 error

Hello All, We try to install bowtie2 package in galaxy but failed. Tool shed: toolshed.g2.bx.psu.edu Name: package_bowtie_2_2_6 Owner: iuc Here is the message: tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract os.chmod( absolute_filepath, unix_permissi

[galaxy-dev] Galaxy CloudMan with Galaxy 16.01

Hello! *We have released a new version of Galaxy CloudMan on AWS.* CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration or imposed quotas. Once runn

Re: [galaxy-dev] perl version 5.18.1 repository error

HHi Marius, Many thanks for this detailed information. I reinstalled the pearl package and it has now the 8.25 version as an additional dependency. The tool seems to work as well. Thanks again, I will ignore the 8.22 version. Cheers, Philipp From: Marius van den Beek [ma

Re: [galaxy-dev] perl version 5.18.1 repository error

Hi Philipp, I believe you have run into a rather complicated problem with perl's dependencies. We (the IUC) have changed from coreutils-8.22 to coreutils-8.25 for exactly the reason you are reporting (`...generated no output for the defined timeout period of 3600.0 seconds`). So you should update

Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01

For us, it was more the fact that we are locked down to a certain OS version due to our local IT policy and the software repositories don't provide a newer Python than v2.6.8. It was not the first occasion in terms of desperately outdated software (recently it's gcc itself), so we are used to compi

Re: [galaxy-dev] Troubleshooting BAM file upload issues

Try using samtools to sort the BAM before uploading. samtools sort original.bam sorted.bam This will help with two things. 1. Check the original file is not corrupt 2. Put the BAM in the only order galaxy will accept. Christian University of Manchester From: g

Re: [galaxy-dev] perl version 5.18.1 repository error

Dear Nicola, now it looks like package_gnu_coreutils_8_22 is generating an error gnu_coreutils 8.22package Error Shutti