Question: on my own computer
gravatar for Mic
3.4 years ago by
Mic70 wrote:

Hello, I like all the tools on and just wondering whether there is anywhere a package which I could download rather to install all tools manually?

galaxy • 724 views
ADD COMMENTlink modified 3.4 years ago by Enis Afgan690 • written 3.4 years ago by Mic70
gravatar for Enis Afgan
3.4 years ago by
Enis Afgan690
United States
Enis Afgan690 wrote:

Take a look a this script:

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:

ADD COMMENTlink written 3.4 years ago by Enis Afgan690

I downloaded the `` and `shed_tool_list.yaml` into galaxy folder. Next, I executed ` -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?  

ADD REPLYlink written 3.4 years ago by Mic70

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 ` -g -a 2ca31d79200d13ecc72346747231ff78 -t shed_tool_list.yaml` . What did I do wrong?


ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Mic70

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

ADD REPLYlink written 3.3 years ago by Mic70
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour