Hi, I have a question regarding tophat2. I would like to add some mammalian genomes to run tophat2/bowtie2 on my local galaxy. I tried using this tutorial: https://wiki.galaxyproject.org/Admin/DataPreparation?action=show&redirect=Admin%2FNGS+Local+Setup but the genomes do not show up in my galaxy. What I did: downloaded the fasta sequences created the bt2 /opt/galaxy/galaxy-dist/tool-data/genome/bta/bowtie2/ total 6861592 -rw-rw-r-- 1 galaxy galaxy 940461913 25. Jun 15:35 bosTau7.1.bt2 -rw-rw-r-- 1 galaxy galaxy 701168300 25. Jun 15:35 bosTau7.2.bt2 -rw-rw-r-- 1 galaxy galaxy 846251 25. Jun 14:31 bosTau7.3.bt2 -rw-rw-r-- 1 galaxy galaxy 701168294 25. Jun 14:31 bosTau7.4.bt2 -rwxr-xr-x 1 galaxy galaxy 3040960704 25. Jun 14:16 bosTau7.fa -rw-rw-r-- 1 galaxy galaxy 940461913 25. Jun 16:36 bosTau7.rev.1.bt2 -rw-rw-r-- 1 galaxy galaxy 701168300 25. Jun 16:36 bosTau7.rev.2.bt2 than modified the bowtie2_indices.loc file like this for each dataset: btabt2 btabt2 Cow(bta7) /opt/galaxy/galaxy-dist/tool-data/genome/bta/bowtie2/bosTau7 after restarting the galaxy I get no genomes for selection under "use a built in genome" "Select a reference genome:" is empty Has anyone suggestions?
First, the path that the data is at has to be accessible by the "galaxy user". Make sure that is true.
Second, the first two columns need to be the same "dbkey" for the genome that you have in your builds.txt file (or the builds tables, depending on which Galaxy version you are running).
Look under the tool "Get Data -> Upload File" for this genome. Has it been added? What did you use for the short name/dbkey (should be a single "word" - no spaces)? In general this is the same as the base name of the genome (so, bosTau7 in your case), so that the genome's dbkey will work with other tools that use it and reference external sites - in particular UCSC for this one. Use that also for the first two columns in this file (exactly, no extra spaces, same capitalization).
Technically the first column is the dbkey and the other is a "display database" metadata attribute, but it is useful to keep these the same unless you have multiple versions of the genome, all using the same dbkey (e.g. subsets of the genome - any other changes will be problematic).
You can check/compare http://usegalaxy.org and our rsync loc files for examples - this genome is included.
Check the builds list in the UI, adjust the loc, restart, and see if that helps. Builds tables are not fully documented in the wiki yet, but we can help with instructions if your genome is not present there.
Thanks! Jen, Galaxy team
I still have no luck with the build-in genomes for tophat2.
My files have real TABs and they are accessible for my galaxy user. The first column and the dbkey are the same like in tool-data/shared/ucsc/build.txt. Or do I need to change the build.txt somewhere else? I also see my changes for my genomes if I look under the tool "Get Data -> Upload File" for this genome.
Maybe I need to set up these so called build tables=?