| Previous changeset 20:ab5e4602bd28 (2017-05-26) |
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Commit message:
Updating README |
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modified:
isoem2_isode2/README.txt |
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| diff -r ab5e4602bd28 -r b07d4238ba9b isoem2_isode2/README.txt --- a/isoem2_isode2/README.txt Fri May 26 10:45:35 2017 -0400 +++ b/isoem2_isode2/README.txt Sun Jun 04 11:10:45 2017 -0400 |
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| @@ -5,8 +5,6 @@ 2) Download and install IsoEM2/IsoDE2 (https://github.com/mandricigor/isoem2) 3) Install other dependencies: -- tmap (needed for ION Torrent data) - Available at https://github.com/iontorrent/TMAP - hisat2 (needed for Illumina data) Available at https://ccb.jhu.edu/software/hisat2/index.shtml - prinseq @@ -16,11 +14,14 @@ 4) Edit isoem_wrapper.sh and IsoDE2.sh. Change tool paths to where they are installed on your system -5) build hisat2 for the reference you will use for mapping +5) Copy .loc file under tool-data directory in Galaxy + +6) build hisat2 for the reference you will use for mapping -6) Edit the .loc file with paths to your reference files: GTF, Transcript to gene cluster, and mapper indices), and copy it under tool-data directory in Galaxy -Note: If you need only one of the two mappers (say hisat2), you can replace the other path to the other maaper index with a dummy path +7) Edit the .loc file with paths to your reference files: GTF, Transcript to gene cluster, and mapper index). -7) copy the entry in the tool_data_table_conf.xml file provided in this repository to the tool_data_table_conf.xml in your Galaxy config directory +Note: steps 6 and 7 are not needed if you will use IsoEM2 option "Use reference from the history" and not "Use a built-in reference" + +8) copy the entry in the tool_data_table_conf.xml file provided in this repository to the tool_data_table_conf.xml in your Galaxy config directory |