[Galaxy rna-workbench] Missing reference data

[mtangaro]

Missing reference data for the following tools:

• RNA-STAR

[mtangaro]

How to manually enable RNA-STAR reference data:

1. Log in the Virtual Instance using SSH.
2. Become super user:

   # sudo su -

3. If you are using the Galaxy Docker Container, enter in the docker with the following command:

   # docker exec -it galaxydocker bash

   If not, skip this step and go to step 4.

4. Check if loc file rnastar_index2.loc is in the path "/cvmfs/data.galaxyproject.org/managed/location" with the following command

   # ll /cvmfs/data.galaxyproject.org/managed/location
   total 280
   -rw-r--r-- 1 cvmfs cvmfs   3772 Nov  6  2018 alignseq.loc
   -rw-r--r-- 1 cvmfs cvmfs   1412 Mar 25 15:36 all_fasta_dbkeys.loc
   -rw-r--r-- 1 cvmfs cvmfs   2996 Mar 25 15:36 all_fasta.loc
   -rw-r--r-- 1 cvmfs cvmfs   6616 Nov  6  2018 bowtie2_indices.loc
   -rw-r--r-- 1 cvmfs cvmfs  67864 Aug  7  2019 builds.txt
   -rw-r--r-- 1 cvmfs cvmfs   8198 Nov  7  2018 bwa_mem_index.loc
   -rw-r--r-- 1 cvmfs cvmfs    491 Mar 26 13:45 dbkeys.loc
   -rw-r--r-- 1 cvmfs cvmfs 138163 Aug  7  2019 dbkeys_ucsc.loc
   -rw-r--r-- 1 cvmfs cvmfs   4274 Nov  6  2018 fasta_indexes.loc
   -rw-r--r-- 1 cvmfs cvmfs   9312 Nov  6  2018 hisat2_indexes.loc
   -rw-r--r-- 1 cvmfs cvmfs    240 Oct 25  2016 kraken_databases.loc
   -rw-r--r-- 1 cvmfs cvmfs   3883 Nov  6  2018 lastz_seqs.loc
   -rw-r--r-- 1 cvmfs cvmfs    100 May 24  2017 ncbi_taxonomy.loc
   -rw-r--r-- 1 cvmfs cvmfs   3772 Nov  6  2018 picard_index.loc
   -rw-r--r-- 1 cvmfs cvmfs    646 Jan  4  2019 plant_tribes_scaffolds.loc
   -rw-r--r-- 1 cvmfs cvmfs   3131 Nov  6  2018 rnastar_index2.loc
   -rw-r--r-- 1 cvmfs cvmfs   5302 Oct 25  2018 tool_data_table_conf.xml
   -rw-r--r-- 1 cvmfs cvmfs   6616 Nov  6  2018 tophat2_indices.loc
   -rw-r--r-- 1 cvmfs cvmfs   2233 Nov  6  2018 twobit.loc
   -rw-r--r-- 1 cvmfs cvmfs  12088 Sep  4  2019 ucsc_build_sites.txt

5. If the file is available, edit /home/galaxy/galaxy/config/tool_data_table_conf.xml file for VM instances or /etc/galaxy/tool_data_table_conf.xml file for Docker instances with your favourite text editor, for example vim or nano, adding the following lines in the <tables>...</tables> section:

   <!-- iobio rnastar servers -->
   <table name="rnastar_index2" comment_char="#" allow_duplicate_entries="False">
   <columns>value, dbkey, name, path, with-gtf</columns>
   <file path="/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2.loc" />
   </table>

6. Save and exit.
7. Restart Galaxy with

   # supervisorctl restart galaxy:

[pmandreoli]

Galaxy reference data update: only STAR wrapper version > 2.7.4a are supported. The one installed on Laniakea Galaxy express RNA-workbench is 2.7.2.

How to fix

1. Install rgrnastar version 2.7.5 , the only one > 2.7.4a and compatible with Galaxy < 20.01.
2. restart galaxy # supervisorctl restart galaxy:. The STAR reference data should be visible again