Using RSEM tool within Trinity we obtained the error "no bowtie-build" in (PATH) as shown below. Can someone tell us what is the problem? Is a tool misconfiguration? or an error in parameter specification? What can we do to fix this? Thanks, Victor Trevino & Jessy Herrera

bowtie2 version 2.3.2 loaded. samtools version 1.5 loaded. jellyfish version 2.2.9 loaded. salmon version 0.9.1 loaded. trinityrnaseq version 2.6.6 loaded. ERROR: which: no bowtie-build in (/N/soft/rhel7/discasm/0.1.2:/N/dc2/projects/galaxyshared/trinity/third_party_applications/STAR-2.6.0c/bin/Linux_x86_64:/N/dc2/projects/galaxyshared/trinity/third_party_applications/GMAP-fusion-v0.4.0:/N/dc2/projects/galaxyshared/trinity/third_party_applications/gmap-2017-11-15/bin:/N/dc2/projects/galaxyshared/trinity/third_party_applications/oases_0.2.8:/N/dc2/projects/galaxyshared/trinity/third_party_applications/velvet_1.2.10:/N/dc2/projects/galaxyshared/trinity/third_party_applications/FusionInspector-v1.3.0:/N/dc2/projects/galaxyshared/trinity/colo/Trinity_CTAT/fusion:/N/soft/rhel7/gatk/4.0.4.0:/N/u/iugalaxy/Karst/galaxy_tools/bowtie-1.2.2-linux-x86_64:/N/soft/rhel7/trinityrnaseq/2.6.6:/N/soft/rhel7/trinityrnaseq/2.6.6/util:/N/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts:/N/soft/rhel7/trinityrnaseq/2.6.6/util:/N/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts:/N/soft/rhel7/trinityrnaseq/2.6.6:/N/soft/rhel7/salmon/0.9.1/bin:/N/soft/rhel7/jellyfish/2.2.9/bin:/N/soft/rhel7/kallisto/gnu/0.43.1/bin:/N/soft/rhel7/hdf5/gnu/serial/1.10.1/bin:/N/soft/rhel7/hisat2/2.1.0/:/N/soft/rhel7/rsem/gnu/1.3.0/:/N/soft/rhel7/star/STAR-2.5.3a/bin/Linux_x86_64:/N/soft/rhel7/tabix/0.2.6/:/N/soft/rhel7/stringtie/1.3.3b:/N/soft/rhel7/samtools/1.5/bin/:/N/soft/rhel7/bedtools/gnu/2.26.0/bin:/N/soft/rhel7/fastqc/0.11.5/:/N/soft/rhel7/bowtie2/intel/2.3.2/:/N/soft/rhel7/java/1.8.0_131/bin:/N/soft/rhel7/perl/gnu/5.24.1/bin:/N/soft/rhel7/r/3.3.1/bin:/N/soft/rhel7/curl/intel/7.54.0/bin:/N/dc2/projects/galaxyshared/trinity/colo/galconf/galaxyPy_Tool/bin:/N/soft/rhel7/git/gnu/2.13.0/bin:/N/soft/rhel7/quotas:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/bin/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/intel64/bin:/N/soft/rhel7/gcc/6.3.0/bin:/opt/moab/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/N/u/trinity/Carbonate/bin:/usr/local/bin)

ERROR, cannot find bowtie-build in PATH setting: /N/soft/rhel7/discasm/0.1.2:/N/dc2/projects/galaxyshared/trinity/third_party_applications/STAR-2.6.0c/bin/Linux_x86_64:/N/dc2/projects/galaxyshared/trinity/third_party_applications/GMAP-fusion-v0.4.0:/N/dc2/projects/galaxyshared/trinity/third_party_applications/gmap-2017-11-15/bin:/N/dc2/projects/galaxyshared/trinity/third_party_applications/oases_0.2.8:/N/dc2/projects/galaxyshared/trinity/third_party_applications/velvet_1.2.10:/N/dc2/projects/galaxyshared/trinity/third_party_applications/FusionInspector-v1.3.0:/N/dc2/projects/galaxyshared/trinity/colo/Trinity_CTAT/fusion:/N/soft/rhel7/gatk/4.0.4.0:/N/u/iugalaxy/Karst/galaxy_tools/bowtie-1.2.2-linux-x86_64:/N/soft/rhel7/trinityrnaseq/2.6.6:/N/soft/rhel7/trinityrnaseq/2.6.6/util:/N/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts:/N/soft/rhel7/trinityrnaseq/2.6.6/util:/N/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts:/N/soft/rhel7/trinityrnaseq/2.6.6:/N/soft/rhel7/salmon/0.9.1/bin:/N/soft/rhel7/jellyfish/2.2.9/bin:/N/soft/rhel7/kallisto/gnu/0.43.1/bin:/N/soft/rhel7/hdf5/gnu/serial/1.10.1/bin:/N/soft/rhel7/hisat2/2.1.0/:/N/soft/rhel7/rsem/gnu/1.3.0/:/N/soft/rhel7/star/STAR-2.5.3a/bin/Linux_x86_64:/N/soft/rhel7/tabix/0.2.6/:/N/soft/rhel7/stringtie/1.3.3b:/N/soft/rhel7/samtools/1.5/bin/:/N/soft/rhel7/bedtools/gnu/2.26.0/bin:/N/soft/rhel7/fastqc/0.11.5/:/N/soft/rhel7/bowtie2/intel/2.3.2/:/N/soft/rhel7/java/1.8.0_131/bin:/N/soft/rhel7/perl/gnu/5.24.1/bin:/N/soft/rhel7/r/3.3.1/bin:/N/soft/rhel7/curl/intel/7.54.0/bin:/N/dc2/projects/galaxyshared/trinity/colo/galconf/galaxyPy_Tool/bin:/N/soft/rhel7/git/gnu/2.13.0/bin:/N/soft/rhel7/quotas:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/bin/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/intel64/bin:/N/soft/rhel7/gcc/6.3.0/bin:/opt/moab/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/N/u/trinity/Carbonate/bin:/usr/local/bin

which: no bowtie in (/N/soft/rhel7/discasm/0.1.2:/N/dc2/projects/galaxyshared/trinity/third_party_applications/STAR-2.6.0c/bin/Linux_x86_64:/N/dc2/projects/galaxyshared/trinity/third_party_applications/GMAP-fusion-v0.4.0:/N/dc2/projects/galaxyshared/trinity/third_party_applications/gmap-2017-11-15/bin:/N/dc2/projects/galaxyshared/trinity/third_party_applications/oases_0.2.8:/N/dc2/projects/galaxyshared/trinity/third_party_applications/velvet_1.2.10:/N/dc2/projects/galaxyshared/trinity/third_party_applications/FusionInspector-v1.3.0:/N/dc2/projects/galaxyshared/trinity/colo/Trinity_CTAT/fusion:/N/soft/rhel7/gatk/4.0.4.0:/N/u/iugalaxy/Karst/galaxy_tools/bowtie-1.2.2-linux-x86_64:/N/soft/rhel7/trinityrnaseq/2.6.6:/N/soft/rhel7/trinityrnaseq/2.6.6/util:/N/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts:/N/soft/rhel7/trinityrnaseq/2.6.6/util:/N/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts:/N/soft/rhel7/trinityrnaseq/2.6.6:/N/soft/rhel7/salmon/0.9.1/bin:/N/soft/rhel7/jellyfish/2.2.9/bin:/N/soft/rhel7/kallisto/gnu/0.43.1/bin:/N/soft/rhel7/hdf5/gnu/serial/1.10.1/bin:/N/soft/rhel7/hisat2/2.1.0/:/N/soft/rhel7/rsem/gnu/1.3.0/:/N/soft/rhel7/star/STAR-2.5.3a/bin/Linux_x86_64:/N/soft/rhel7/tabix/0.2.6/:/N/soft/rhel7/stringtie/1.3.3b:/N/soft/rhel7/samtools/1.5/bin/:/N/soft/rhel7/bedtools/gnu/2.26.0/bin:/N/soft/rhel7/fastqc/0.11.5/:/N/soft/rhel7/bowtie2/intel/2.3.2/:/N/soft/rhel7/java/1.8.0_131/bin:/N/soft/rhel7/perl/gnu/5.24.1/bin:/N/soft/rhel7/r/3.3.1/bin:/N/soft/rhel7/curl/intel/7.54.0/bin:/N/dc2/projects/galaxyshared/trinity/colo/galconf/galaxyPy_Tool/bin:/N/soft/rhel7/git/gnu/2.13.0/bin:/N/soft/rhel7/quotas:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/bin/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/intel64/bin:/N/soft/rhel7/gcc/6.3.0/bin:/opt/moab/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/N/u/trinity/Carbonate/bin:/usr/local/bin)

ERROR, cannot find bowtie in PATH setting: /N/soft/rhel7/discasm/0.1.2:/N/dc2/projects/galaxyshared/trinity/third_party_applications/STAR-2.6.0c/bin/Linux_x86_64:/N/dc2/projects/galaxyshared/trinity/third_party_applications/GMAP-fusion-v0.4.0:/N/dc2/projects/galaxyshared/trinity/third_party_applications/gmap-2017-11-15/bin:/N/dc2/projects/galaxyshared/trinity/third_party_applications/oases_0.2.8:/N/dc2/projects/galaxyshared/trinity/third_party_applications/velvet_1.2.10:/N/dc2/projects/galaxyshared/trinity/third_party_applications/FusionInspector-v1.3.0:/N/dc2/projects/galaxyshared/trinity/colo/Trinity_CTAT/fusion:/N/soft/rhel7/gatk/4.0.4.0:/N/u/iugalaxy/Karst/galaxy_tools/bowtie-1.2.2-linux-x86_64:/N/soft/rhel7/trinityrnaseq/2.6.6:/N/soft/rhel7/trinityrnaseq/2.6.6/util:/N/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts:/N/soft/rhel7/trinityrnaseq/2.6.6/util:/N/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts:/N/soft/rhel7/trinityrnaseq/2.6.6:/N/soft/rhel7/salmon/0.9.1/bin:/N/soft/rhel7/jellyfish/2.2.9/bin:/N/soft/rhel7/kallisto/gnu/0.43.1/bin:/N/soft/rhel7/hdf5/gnu/serial/1.10.1/bin:/N/soft/rhel7/hisat2/2.1.0/:/N/soft/rhel7/rsem/gnu/1.3.0/:/N/soft/rhel7/star/STAR-2.5.3a/bin/Linux_x86_64:/N/soft/rhel7/tabix/0.2.6/:/N/soft/rhel7/stringtie/1.3.3b:/N/soft/rhel7/samtools/1.5/bin/:/N/soft/rhel7/bedtools/gnu/2.26.0/bin:/N/soft/rhel7/fastqc/0.11.5/:/N/soft/rhel7/bowtie2/intel/2.3.2/:/N/soft/rhel7/java/1.8.0_131/bin:/N/soft/rhel7/perl/gnu/5.24.1/bin:/N/soft/rhel7/r/3.3.1/bin:/N/soft/rhel7/curl/intel/7.54.0/bin:/N/dc2/projects/galaxyshared/trinity/colo/galconf/galaxyPy_Tool/bin:/N/soft/rhel7/git/gnu/2.13.0/bin:/N/soft/rhel7/quotas:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/bin/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/intel64/bin:/N/soft/rhel7/gcc/6.3.0/bin:/opt/moab/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/N/u/trinity/Carbonate/bin:/usr/local/bin

Please be sure bowtie and express are installed and the utilities samtools bowtie-build bowtie rsem-calculate-expression are available via your PATH setting.

bowtie2 version 2.3.2 loaded. samtools version 1.5 loaded. jellyfish version 2.2.9 loaded. salmon version 0.9.1 loaded. trinityrnaseq version 2.6.6 loaded.

Hello,

My guess is that there are dependency disconnect problems, but OS could be a factor. You have checked that these are all present with the correct permissions in the PATH settings the "galaxy user" accesses? The bowtie version appears to not be in sync (version 1.x and version 2.x are not the same). Maybe try installing Bowtie (v1) as a first pass at a fix?

If that does not resolve the problem, please share more details and we can get the developers involved in case there is a problem with a repository or simply help to get this configured correctly. Include back as a comment:

• What version of Galaxy are you running (and local or docker?)
• When did you last check for point updates?
• Which ToolShed tool repositories did you install?

Links to the repositories is a good way to share exactly what your environment is like for these factors and will help with troubleshooting if needed.

Thanks! Jen, Galaxy team