bigwig problem

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bigwig problem

Jochen Bick
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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Re: bigwig problem

Nate Coraor (nate@bx.psu.edu)
Hi Jochen,

I ran in to this yesterday, we're working on fixing it right now. It's due to this:


And because Galaxy's converters use the `ucsc_tools` IUC conda metapackage, which still points to the old versions. I have an update here:


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 <[hidden email]> 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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Re: bigwig problem

Jochen Bick
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
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Re: bigwig problem

Jochen Bick
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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Re: bigwig problem

Nate Coraor (nate@bx.psu.edu)
In reply to this post by Jochen Bick
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 <[hidden email]> 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
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Re: bigwig problem

Nate Coraor (nate@bx.psu.edu)
In reply to this post by Jochen Bick
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 <[hidden email]> 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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: bigwig problem

Jochen Bick

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 <[hidden email]> 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/[hidden email]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/[hidden email]trinity-2.4.0/PerlLib/Pipeliner.pm
line 166.
        Pipeliner::run(Pipeliner=HASH(0xd8f630)) called at
/opt/galaxy/production/_conda/[hidden email]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/[hidden email]Trinity line 1595
        main::run_Trinity() called at
/opt/galaxy/production/_conda/[hidden email]Trinity line 1262
        eval {...} called at
/opt/galaxy/production/_conda/[hidden email]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
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Re: bigwig problem

Jochen Bick
In reply to this post by Nate Coraor (nate@bx.psu.edu)

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 <[hidden email]> 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/[hidden email]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/[hidden email]trinity-2.4.0/PerlLib/Pipeliner.pm
line 166.
        Pipeliner::run(Pipeliner=HASH(0xd8f630)) called at
/opt/galaxy/production/_conda/[hidden email]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/[hidden email]Trinity line 1595
        main::run_Trinity() called at
/opt/galaxy/production/_conda/[hidden email]Trinity line 1262
        eval {...} called at
/opt/galaxy/production/_conda/[hidden email]Trinity line 1261

Trinity run failed. Must investigate error above.


has anyone got an idea?

Cheers Jochen
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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___________________________________________________________
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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