Hej Nate,

thanks, how to I install this on the galaxy specific conda? I have at least 3 different conda version on my machine and also two galaxy servers running. the last time i tried to update one of the packages inside conda I broke the complete conda somehow...

Cheers Jochen

This occurs when bzip2 is installed from defaults instead of conda-forge. If you have Conda >= 4.0 this shouldn't happen as long as you install with the right channel order e.g. `-c iuc -c bioconda -c conda-forge -c defaults`. You should be able to fix this one with:

  conda install -n __trinity@2.4.0 -c conda-forge bzip2=1.0.6=1

--nate

On Thu, Mar 1, 2018 at 10:41 AM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:

Hej all,

I'm also facing another problem which might be related to my previous
error, when I run Trinity:

samtools: error while loading shared libraries: libbz2.so.1.0: cannot
open shared object file: No such file or directory
samtools: error while loading shared libraries: libbz2.so.1.0: cannot
open shared object file: No such file or directory
Error outputting data
Error: Encountered internal Bowtie 2 exception (#1)
Command:
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/bowtie2-align-s
--wrapper basic-0 --local -k 2 --threads 5 -f --score-min G,46,0 -x
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/both.fa

(ERR): bowtie2-align exited with value 1
Error, cmd: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 5
-f --score-min G,46,0 -x
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/both.fa
 | samtools view -@ 5 -F4 -Sb - | samtools sort -m 107374182 -@ 5 -no -
- >
/opt/galaxy/production/galaxy-dist/database/jobs_directory/018/18987/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"
 2>tmp.54212.stderr died with ret 32512 at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/opt/trinity-2.4.0/PerlLib/Pipeliner.pm
line 166.
        Pipeliner::run(Pipeliner=HASH(0xd8f630)) called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1750
        main::run_chrysalis("/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"..., "/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"..., 200, 500, "RF", "/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"..., "/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...) called at /opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1595
        main::run_Trinity() called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1262
        eval {...} called at
/opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1261

Trinity run failed. Must investigate error above.


has anyone got an idea?

Cheers Jochen

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