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 On 02.03.2018 17:49, Nate Coraor wrote:
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 <mailto: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 ___________________________________________________________ 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/ <https://lists.galaxyproject.org/>
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