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 [email protected] -c conda-forge bzip2=1.0.6=1
--nate
On Thu, Mar 1, 2018 at 10:41 AM, Jochen Bick <[email protected]
<mailto:[email protected]>> 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/[email protected]/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/[email protected]/opt/trinity-2.4.0/PerlLib/Pipeliner.pm
line 166.
Pipeliner::run(Pipeliner=HASH(0xd8f630)) called at
/opt/galaxy/production/_conda/envs/[email protected]/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/[email protected]/bin/Trinity
line 1595
main::run_Trinity() called at
/opt/galaxy/production/_conda/envs/[email protected]/bin/Trinity
line 1262
eval {...} called at
/opt/galaxy/production/_conda/envs/[email protected]/bin/Trinity
line 1261
Trinity run failed. Must investigate error above.
has anyone got an idea?
Cheers Jochen
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