Hi,
how can I fix this problem?
bedGraphToBigWig: error while loading shared libraries: libmysqlclient.so.18: cannot open shared object file: No such file or directory
I have the files in the local bin but somehow it does not work inside galaxy.
Thanks in advance. Cheers Jochen
Hi Jochen,
I ran in to this yesterday, we're working on fixing it right now. It's due to this:
https://github.com/bioconda/bioconda-recipes/issues/5430
And because Galaxy's converters use the `ucsc_tools` IUC conda metapackage, which still points to the old versions. I have an update here:
https://github.com/galaxyproject/conda-iuc/pull/14
Once that is available you should be able to `conda update ucsc_tools` the affected environments. I am also working on switching all of the requirements so they depend on the individual ucsc-* packages from Bioconda instead of the metapackage so we shouldn't need to maintain it in the future.
--nate
On Thu, Feb 15, 2018 at 10:17 AM, Jochen Bick jochen.bick@usys.ethz.ch wrote:
Hi,
how can I fix this problem?
bedGraphToBigWig: error while loading shared libraries: libmysqlclient.so.18: cannot open shared object file: No such file or directory
I have the files in the local bin but somehow it does not work inside galaxy.
Thanks in advance. Cheers Jochen
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Thanks, nate,
can you tell me one I can update? And what i need to update?
Cheers Jochen
On 15.02.2018 16:24, Nate Coraor wrote:
Hi Jochen,
I ran in to this yesterday, we're working on fixing it right now. It's due to this:
https://github.com/bioconda/bioconda-recipes/issues/5430
And because Galaxy's converters use the `ucsc_tools` IUC conda metapackage, which still points to the old versions. I have an update here:
https://github.com/galaxyproject/conda-iuc/pull/14
Once that is available you should be able to `conda update ucsc_tools` the affected environments. I am also working on switching all of the requirements so they depend on the individual ucsc-* packages from Bioconda instead of the metapackage so we shouldn't need to maintain it in the future.
--nate
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
What I ended up doing was downgrading MySQL to 5.6 in the affected environments.
On Tue, Feb 20, 2018 at 4:51 AM, Jochen Bick jochen.bick@usys.ethz.ch wrote:
Thanks, nate,
can you tell me one I can update? And what i need to update?
Cheers Jochen
On 15.02.2018 16:24, Nate Coraor wrote:
Hi Jochen,
I ran in to this yesterday, we're working on fixing it right now. It's
due
to this:
https://github.com/bioconda/bioconda-recipes/issues/5430
And because Galaxy's converters use the `ucsc_tools` IUC conda
metapackage,
which still points to the old versions. I have an update here:
https://github.com/galaxyproject/conda-iuc/pull/14
Once that is available you should be able to `conda update ucsc_tools`
the
affected environments. I am also working on switching all of the requirements so they depend on the individual ucsc-* packages from
Bioconda
instead of the metapackage so we shouldn't need to maintain it in the future.
--nate
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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 ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
Hi,
I could solve the problem with bzip. Now this part is working.
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/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
galaxy-dev@lists.galaxyproject.org
-
Jochen Bick -
Nate Coraor