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

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