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gvlproject / gvl.ansible.playbook

Playbook for building the Genomics Virtual Laboratory
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GVL-4.1 no visualisation for hg38 and some other assemblies on UCSC genome browser #42

Closed igormakunin closed 8 years ago

igormakunin commented 8 years ago

Data for some genome assemblies, including the latest human genome hg38, are not displayed on UCSC genome browser. It would be useful to have links to UCSC for assemblies with build-in genome indices provided by GVL.

Fix: /mnt/galaxy/galaxy-app/tool-data/shared/ucsc/ucsc_build_sites.txt Add sacCer2,sacCer3,hg38,bosTau7,rn6,rn5,oviAri3,ce10,danRer7 to 'main' line. I have impression the position is irrelevant.

Also, it is impossible to assign sacCer3 and ce10 to uploaded files, but GVL provides indices for these assemblies. To fix the issue add: ce10 C. elegans Oct 2010 (WS220/ce10) (ce10) sacCer3 S. cerevisiae Apr 2011 (SacCer_Apr2011/saCer3) (sacCer3) to: /mnt/galaxy/galaxy-app/tool-data/shared/ucsc/builds.txt NOTE: it has to be TAB-separated

nuwang commented 8 years ago

Fixed in commit: https://github.com/gvlproject/gvl.ansible.filesystem/commit/1413a8a9a7d5bc012db4311f2ffe049f308f5b76

nuwang commented 8 years ago

@igormakunin Will move to in-test and assign to you once latest build is complete.