Hello, I like all the tools on usegalaxy.org and just wondering whether there is anywhere a package which I could download rather to install all tools manually?
Take a look a this script: https://github.com/galaxyproject/ansible-cloudman-galaxy-setup/blob/master/files/scripts/install_tool_shed_tools.py
Provided a YAML file with the specifics of the tools, it will install all of them on the target Galaxy instance. A YAML file with all the tools that are installed on Main is available here: https://github.com/galaxyproject/galaxy-cloudman-playbook/blob/master/files/shed_tool_list.yaml
I downloaded the `install_tool_shed_tools.py` and `shed_tool_list.yaml` into galaxy folder. Next, I executed `install_tool_shed_tools.py -t shed_tool_list.yaml` but I have got this error `bioblend.galaxy.client.ConnectionError: ('Connection aborted.', gaierror(-2, 'Name or service not known')), 0 attempts left: None`. How is it possible to fix the error?
I have got the script running, but the tools are not visible in Galaxy after I received the following output "All tools listed in 'shed_tool_list.yaml' have been processed". This is the command `install_tool_shed_tools.py -g http://127.0.0.1:8080 -a 2ca31d79200d13ecc72346747231ff78 -t shed_tool_list.yaml` . What did I do wrong?
The script installed 205 out of 230 tools. However, the tools are not categorized i.e. BWA, Bowtie2, ... are not in NGS:Mapping. These are the tools which failed to install: ('fastq_trimmer_by_quality', '1cdcaf5fc1da'), ('vcffilter', '34c3b846e0b6'), ('annotation_profiler', '3b33da018e74'), ('hgv_hilbertvis', 'e1a9ad05dced'), ('kernel_canonical_correlation_analysis', '7a092113eb8c'), ('fasta_compute_length', '1dbb5181c327'), ('clustalw', 'acf51ff24c7d'), ('samtools_rmdup', '3735f950b2f5'), ('sam_merge', 'a7a49d31c5cf'), ('macs', 'ae2ec275332a'), ('sicer', '82a8234e03f2'), ('naive_variant_caller', '907b40517289'), ('tophat2', '6242cda7e278'), ('cuffdiff', '4e6f043995ff'), ('cuffdiff', 'db57b46b05bf'), ('tophat_fusion_post', 'f83394a2c2da'), ('variants_validate', '7e1ecaa64370'), ('variant_select', '135e8721ffc5'), ('variant_filtration', 'da6e2503c62d'), ('variant_annotator', 'ae9d0a543e9b'), ('unified_genotyper', '66dd4d4c1743'), ('indel_realigner', 'bb0beda6cf83'), ('htseq_bams_to_count_matrix', u'e34313b3898b'), ('data_manager_rsync_g2', u'fc28d0b1e074'), ('data_manager_picard_index_builder', u'7a5d54135791'). By any chance, does anyone know which yaml has to be used to get the same heading for tools like usegalaxy.org?
