HI,
Bug in latest Hisat2 tool.
Hisat2 tool version 2.0.3 revision 2d449a1bb5ab does not attempt to
setup the environment in tool_script.sh and job stops with error:
Fatal error: Exit code 127 ()
/home/galaxy/database/jobs_directory/000/497/tool_script.sh: line 9:
hisat2-build: command not found
tool_script.sh:
PACKAGE_BASE=/home/galaxy/tools/dependencies/samtools/1.2/iuc/hisat2/
2d449a1bb5ab; export PACKAGE_BASE; .
/home/galaxy/tools/dependencies/samtools/1.2/iuc/hisat2/2d449a1bb5ab/e
nv.sh; hisat2 --version >
/home/galaxy/database/tmp/GALAXY_VERSION_STRING_500 2>&1; ln -s
"/home/genomes/caenorhabditis_elegans/release-84/Caenorhabditis_elega
ns.WBcel235.dna.toplevel.fa" genome.fa && hisat2-build genome.fa
genome && hisat2 -p ${GALAXY_SLOTS:-1} -x "genome" -U
"/home/galaxy/database/files/001/dataset_1034.dat" -k 5 | samtools sort - -
@ ${GALAXY_SLOTS:-2} -l 6 -o hsbam >
"/home/galaxy/database/files/001/dataset_1674.dat"
Hisat2 tool version 2.0 revision b1e25f9b5eab works okay and create next
tool_script.sh:
PACKAGE_BASE=/home/galaxy/tools/dependencies/hisat/2.0/iuc/hisat2/b1e
25f9b5eab; export PACKAGE_BASE; .
/home/galaxy/tools/dependencies/hisat/2.0/iuc/hisat2/b1e25f9b5eab/env.s
h;
PACKAGE_BASE=/home/galaxy/tools/dependencies/samtools/1.2/iuc/hisat2/
b1e25f9b5eab; export PACKAGE_BASE; .
/home/galaxy/tools/dependencies/samtools/1.2/iuc/hisat2/b1e25f9b5eab/e
nv.sh; hisat2 --version >
/home/galaxy/database/tmp/GALAXY_VERSION_STRING_501 2>&1; ln -s
"/home/genomes/caenorhabditis_elegans/release-84/Caenorhabditis_elega
ns.WBcel235.dna.toplevel.fa" genome.fa && hisat2-build genome.fa
genome && hisat2 -p ${GALAXY_SLOTS:-1} -x "genome" -U
"/home/galaxy/database/files/001/dataset_1034.dat" -k 5 | samtools sort - -
@ ${GALAXY_SLOTS:-2} -l 6 -o hsbam >
"/home/galaxy/database/files/001/dataset_1675.dat"
Galaxy is:
Merge branch 'release_16.04'
Probably it can be solve quickly by correction of config files. Does someone
know where to look to solve such kind of problems?
Thanx,
Nick
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
