Hi Galaxy, I am trying to install HISAT2 from the toolshed to my Cloudman instance (revision da2cc588e5) and not succeeding.
When I try to install HISAT2 from the toolshed one of the packages gets hung up (I think 'ncurses'), but if I go back one page and re-click the install button enough times I can get HISAT2 to the 'installed' state and it shows up in my tool panel. I can then install data managers and get the appropriate HISAT2 index installed. When I try running HISAT2 on some small sample data I get the following error:
Fatal error: Matched on hisat2-align exited with value 1
Error reading _plen array: 0, 17179869180
Error: Encountered internal HISAT exception (#1)
Command: /mnt/galaxy/tools/hisat/2.0/iuc/package_hisat_2_0/c65f00072e57/bin/hisat2-align-s --wrapper basic-0 -p 1 -x /mnt/galaxyIndices/hg19/hisat2_index/hg19ID/hg19ID -k 5 --n-ceil C,0,0 --pen-cansplice 0 --pen-noncansplice 3 --pen-canintronlen C,0,0 --pen-noncanintronlen C,-8,1 --min-intronlen 20 --max-intronlen 500000 --rna-strandness R -1 /mnt/galaxy/files/003/dataset_3659.dat -2 /mnt/galaxy/files/003/dataset_3657.dat
(ERR): hisat2-align exited with value 1
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
[bam_header_read] EOF marker is absent. The input is probably truncated.
I understand the way I am installing HISAT2 from the toolshed is not optimal. If anyone has had success installing and using HISAT2 on Galaxy Cloumdman could you share your protocol?