Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,

just to mention that deseq2-1-8-2 (requiring r-3-2-1) also installs fine!

Best regards,
Hans
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi Marius,

I bow to your efforts in appreciation - it seems to install without flaws!!

I tried the new cairo-1-12-14 and then r-3-2-1 in a frest postgresqldb/galaxy 
instance … everything got installed and shows the green label ;-)

requirements on top of Mac OS Xcode/command line tools are:
- gfortran (I used the OS X 10.11  gfortran 5.2 installer from here 
https://gcc.gnu.org/wiki/GFortranBinaries 
)
- libiconv-1.14 (from http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz 
) - (which I put into 
/usr/local where it seems to be found without editing my $PATH)

This is great! Many thanks again!
Hans


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Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?

[Björn Grüning]

Hi Bob,

you could write a special visualisation for your specific datatype. This
does not work with the eyeball, but with the visualisation button
associated to every dataset.

For a few visualisation examples please see the following links:

*
https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations
* https://github.com/bgruening/galaxytools/tree/master/visualisations
* https://wiki.galaxyproject.org/VisualizationsRegistry/Cookbook

Hope this gets you started!
Bjoern

> Good afternoon,
> 
> I am trying create a display module for a special binary datatype.
> When someone requests to view the output file in the History using
> the eyeball it will kick off my code to create an HTML display in the
> Galaxy center section.   I am looking at binary.py but I am not sure
> if this is it.  Is there sample or existing code to look at?
> 
> I hope this makes sense to someone on the team.
> 
> Thanks, bob
> 
> 
> 
> ___ Please
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[galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?

[rbrown1422]

Good afternoon,

I am trying create a display module for a special binary datatype.  When 
someone requests to view the output file in the History using the eyeball it 
will kick off my code to create an HTML display in the Galaxy center section.   
I am looking at binary.py but I am not sure if this is it.  Is there sample or 
existing code to look at?

I hope this makes sense to someone on the team.

Thanks,
bob___
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Re: [galaxy-dev] wolfpsort

[Olivier CLAUDE]

Everything is working fine now.
I experienced problems : I forgot to delete some files this made a conflict.
If anybody needs, the python script has to be in the bin folder of the computer 
not  in the HOME folder  (I've made a mistake with the tilde)
Thanks again, normally I will not bother you anymore Peter.

Regards,

Olivier.

-Message d'origine-
De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : vendredi 4 décembre 2015 15:17
À : Olivier CLAUDE 
Cc : galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] wolfpsort

On Fri, Dec 4, 2015 at 12:59 PM, Olivier CLAUDE  wrote:
> Ok i did not saw it.
> I runned it with ./ and it worked fine. It gave me the same answer you gave 
> me earlier.
>
> Olivier

Excellent :)

So, this matches what I found - as long as I changed to the Wolf PSORT 
directory first, runWolfPsortSummary worked OK.

If I just put the runWolfPsortSummary bin folder on the $PATH, then it failed.

Perhaps there is a small step in the instructions we both missed?

I suggest you try my workaround, which I linked to before:
https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/wolf_psort.py#L43

(1) put runWolfPsortSummary somewhere where your cluster nodes and Galaxy can 
see it. I used the folder /opt/WoLFPSORT_package_v0.2/ meaning 
/opt/WoLFPSORT_package_v0.2/bin/runWolfPsortSummary
is the script itself.

Your folder ~/galaxy/CBS/WoLFPSort-master/ would be fine.

(2) Using a text editor (emacs, nano, vi, etc) create a new file named 
runWolfPsortSummary (without an extension) somewhere on your path, I suggest 
~/bin/runWolfPsortSummary

$ emacs ~/bin/runWolfPsortSummary

(3) Copy this into the ~/bin/runWolfPsortSummary file,

#!/usr/bin/env python
#Wrapper script to call WoLF PSORT from its own directory.
import os
import sys
import subprocess
saved_dir = os.path.abspath(os.curdir)
os.chdir("/opt/WoLFPSORT_package_v0.2/bin")
args = ["./runWolfPsortSummary"] + sys.argv[1:] return_code = 
subprocess.call(args)
os.chdir(saved_dir)
sys.exit(return_code)

(3) Mark this wrapper script as executable:

$ chmod a+x ~/bin/runWolfPsortSummary

(4) Check ~/bin is on your path, so that using runWolfPsortSummary (without a 
leading dot slash) will run the new wrapper script:

$ which runWolfPsortSummary
~/bin/runWolfPsortSummary

(5) Test the new wrapper script from some other directory, e.g.

$ cd ~
$ runWolfPsortSummary animal <~/galaxy/test-data/four_human_proteins.fasta

(6) If that all works, then the Galaxy wrapper should work too.

Peter
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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

[Björn Grüning]

Hi Makis,

as a small pointer, please have a look at the ansible playrole we provide:

https://github.com/galaxyproject/ansible-galaxy-extras

or the Galaxy Docker Image:

https://github.com/bgruening/docker-galaxy-stable

all steps are described here and can be reused.
Cheers,
Bjoern

Am 04.12.2015 um 08:39 schrieb Makis Ladoukakis:
> Sorry for bumping my own question but I didn't get any replies. Has anyone 
> succesfully installed a production Galaxy instance? 
> 
> I could really use some advice.
> 
> Thank you,
> Makis
> 
> From: makis4e...@hotmail.com
> To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
> Date: Tue, 1 Dec 2015 18:03:44 +0200
> Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed
> 
> 
> 
> 
> Hello everyone,
> 
> I am trying to setup a Galaxy instance for a multi-user production 
> environment and I tried to follow the instructions here:
> 
> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
> 
> but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
> --daemon) I got the following error in my browser:Bad Gateway
> The proxy server received an invalid
> response from an upstream server.
> 
> 
> I don't get any errors from the paster.log files so I am guessing the error 
> is somewhere in my apache configuration although I can't see where it could 
> be.
> 
> 
> Has anyone encountered this problem before?
> 
> Kind regards,
> Makis
> 
> 
> P.S. My apache configuration is as follows:
> 
> I added that to my apache httpd.conf file:
> 
> #for galaxy
> #RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*) 
> /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/galaxy/static/scripts/(.*) 
> /home/galaxy/galaxy/static/scripts/packed/$1 [L]
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
> RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico 
> [L]
> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]
> 
> LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so
> 
> 
> Sethandler uwsgi-handler
> uWSGISocket 127.0.0.1:4001
> uWSGImaxVars 512
> 
> 
> I am also attaching my job_conf.xml and galaxy.ini file.
> 
> 
> 
> ___
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>   
> 
> 
> 
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Martin Čech]

Awesome Marius, thank you very much for looking into this! M.

On Fri, Dec 4, 2015 at 12:30 PM Marius van den Beek 
wrote:

> Hello Hans (and other OS X users),
>
> I hope that the last remaining problem should be fixed now.
> There is a new revision of package_r_3_2_1 and package_cairo_1_12_14 on
> the toolshed.
> Make sure you get package_cairo_1_12_14 first when you upgrade.
> The underlying problem was that cairo was missing the fontconfig
> dependency,
> which would still compile correctly, but fail when R is built with
> `--with-cairo`.
>
> Cheers,
> Marius
>
> On 4 December 2015 at 09:47, Marius van den Beek 
> wrote:
>
>> Hello Hans,
>>
>> I'm not sure if it would help to use the pre-compiled binaries,
>> as you would still need some of the underlying libraries for building
>> R packages. We're not far from having this fixed ... there is a newer
>> revision of R on the main toolshed,
>> that nevertheless will (probably) fail because of a missing include of
>> what seems to be fontconfig.
>> I had it working yesterday already, I'm trying to see what went wrong in
>> the meantime ...
>>
>> Marius
>>
>> On 4 December 2015 at 09:20, Hans Rudolph  wrote:
>>
>>> Hi,
>>>
>>> I now learned that R-3.2.2 binaries for Mac OS X are available (
>>> https://cran.r-project.org/bin/macosx/) - could that be a potential
>>> help for R-related problems in galaxy on Mac OS X?
>>>
>>> Cheers,
>>> Hans
>>
>>
>>
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Marius van den Beek]

Hello Hans (and other OS X users),

I hope that the last remaining problem should be fixed now.
There is a new revision of package_r_3_2_1 and package_cairo_1_12_14 on the
toolshed.
Make sure you get package_cairo_1_12_14 first when you upgrade.
The underlying problem was that cairo was missing the fontconfig dependency,
which would still compile correctly, but fail when R is built with
`--with-cairo`.

Cheers,
Marius

On 4 December 2015 at 09:47, Marius van den Beek 
wrote:

> Hello Hans,
>
> I'm not sure if it would help to use the pre-compiled binaries,
> as you would still need some of the underlying libraries for building
> R packages. We're not far from having this fixed ... there is a newer
> revision of R on the main toolshed,
> that nevertheless will (probably) fail because of a missing include of
> what seems to be fontconfig.
> I had it working yesterday already, I'm trying to see what went wrong in
> the meantime ...
>
> Marius
>
> On 4 December 2015 at 09:20, Hans Rudolph  wrote:
>
>> Hi,
>>
>> I now learned that R-3.2.2 binaries for Mac OS X are available (
>> https://cran.r-project.org/bin/macosx/) - could that be a potential help
>> for R-related problems in galaxy on Mac OS X?
>>
>> Cheers,
>> Hans
>
>
>
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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

[Peter van Heusden]

I've written up my experiences in a blog:

http://pvh.wp.sanbi.ac.za/2015/12/04/faster-galaxy-with-uwsgi/

The only Galaxy side changes were the ones mentioned on the Scaling page.
The Bad Gateway message means that Apache can't talk to the uWSGI so what
is the state of uWSGI?

Are you using supervisord? Does supervisorctl show the uWSGI process
running? Does ps ax |grep uwsgi show it running? What does sudo lsof -i
:4001 show is listening on port 4001? That would be the starting point of
my debugging.

Peter
On 4 Dec 2015 10:57, "Makis Ladoukakis"  wrote:

> It is uwsgi that I am trying but with apache. Could you let me know what
> changes you made to the configuration of Galaxy?
>
> Thank you,
> Makis
>
> --
> Date: Fri, 4 Dec 2015 10:01:56 +0200
> Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed
> From: p...@sanbi.ac.za
> To: makis4e...@hotmail.com
> CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
>
> Hi Makis, I recently implemented something like this using uWSGI with a
> nginx frontend. Would you consider using uWSGI instead of your current
> approach?
> On 4 Dec 2015 09:40, "Makis Ladoukakis"  wrote:
>
> Sorry for bumping my own question but I didn't get any replies. Has anyone
> succesfully installed a production Galaxy instance?
>
> I could really use some advice.
>
> Thank you,
> Makis
>
> --
> From: makis4e...@hotmail.com
> To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
> Date: Tue, 1 Dec 2015 18:03:44 +0200
> Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed
>
> Hello everyone,
>
> I am trying to setup a Galaxy instance for a multi-user production
> environment and I tried to follow the instructions here:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
>
> but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh
> --daemon) I got the following error in my browser:Bad Gateway The proxy
> server received an invalid response from an upstream server.
>
>
> I don't get any errors from the paster.log files so I am guessing the
> error is somewhere in my apache configuration although I can't see where it
> could be.
>
>
> Has anyone encountered this problem before?
>
> Kind regards,
> Makis
>
>
> P.S. My apache configuration is as follows:
>
> I added that to my apache httpd.conf file:
>
> #for galaxy
> #RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*)
> /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/galaxy/static/scripts/(.*)
> /home/galaxy/galaxy/static/scripts/packed/$1 [L]
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
> RewriteRule ^/galaxy/favicon.ico
> /home/galaxy/galaxy/static/favicon.ico [L]
> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt
> [L]
>
> LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so
>
> 
> Sethandler uwsgi-handler
> uWSGISocket 127.0.0.1:4001
> uWSGImaxVars 512
> 
>
> I am also attaching my job_conf.xml and galaxy.ini file.
>
>
> ___ 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/mailinglists/
>
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>
>
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Re: [galaxy-dev] wolfpsort

[Peter Cock]

On Fri, Dec 4, 2015 at 2:16 PM, Peter Cock  wrote:
> On Fri, Dec 4, 2015 at 12:59 PM, Olivier CLAUDE  wrote:
>> Ok i did not saw it.
>> I runned it with ./ and it worked fine. It gave me the same answer you gave 
>> me earlier.
>>
>> Olivier
>
> Excellent :)
>
> So, this matches what I found - as long as I changed to the Wolf PSORT
> directory first, runWolfPsortSummary worked OK.
>
> If I just put the runWolfPsortSummary bin folder on the $PATH, then it
> failed.
>
> Perhaps there is a small step in the instructions we both missed?
>
> I suggest you try my workaround, which I linked to before:
> https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/wolf_psort.py#L43
>
> (1) put runWolfPsortSummary somewhere where your cluster nodes
> and Galaxy can see it. I used the folder /opt/WoLFPSORT_package_v0.2/
> meaning /opt/WoLFPSORT_package_v0.2/bin/runWolfPsortSummary
> is the script itself.
>
> Your folder ~/galaxy/CBS/WoLFPSort-master/ would be fine.
>
> (2) Using a text editor (emacs, nano, vi, etc) create a new file named
> runWolfPsortSummary (without an extension) somewhere on your
> path, I suggest ~/bin/runWolfPsortSummary
>
> $ emacs ~/bin/runWolfPsortSummary
>
> (3) Copy this into the ~/bin/runWolfPsortSummary file,
>
> #!/usr/bin/env python
> #Wrapper script to call WoLF PSORT from its own directory.
> import os
> import sys
> import subprocess
> saved_dir = os.path.abspath(os.curdir)
> os.chdir("/opt/WoLFPSORT_package_v0.2/bin")
> args = ["./runWolfPsortSummary"] + sys.argv[1:]
> return_code = subprocess.call(args)
> os.chdir(saved_dir)
> sys.exit(return_code)

Sorry, you'd need to change the change director line to match your setup.
You can't use the tilde (~) or $HOME here, so something like this I guess:

os.chdir("/home/x/galaxy/CBS/WoLFPSort-master/")

> (3) Mark this wrapper script as executable:
>
> $ chmod a+x ~/bin/runWolfPsortSummary
>
> (4) Check ~/bin is on your path, so that using runWolfPsortSummary
> (without a leading dot slash) will run the new wrapper script:
>
> $ which runWolfPsortSummary
> ~/bin/runWolfPsortSummary
>
> (5) Test the new wrapper script from some other directory, e.g.
>
> $ cd ~
> $ runWolfPsortSummary animal <~/galaxy/test-data/four_human_proteins.fasta
>
> (6) If that all works, then the Galaxy wrapper should work too.
>
> Peter

I filed this as an issue on the GitHub mirror:

https://github.com/fmaguire/WoLFPSort/issues/1

Peter
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Re: [galaxy-dev] wolfpsort

[Peter Cock]

On Fri, Dec 4, 2015 at 12:59 PM, Olivier CLAUDE  wrote:
> Ok i did not saw it.
> I runned it with ./ and it worked fine. It gave me the same answer you gave 
> me earlier.
>
> Olivier

Excellent :)

So, this matches what I found - as long as I changed to the Wolf PSORT
directory first, runWolfPsortSummary worked OK.

If I just put the runWolfPsortSummary bin folder on the $PATH, then it
failed.

Perhaps there is a small step in the instructions we both missed?

I suggest you try my workaround, which I linked to before:
https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/wolf_psort.py#L43

(1) put runWolfPsortSummary somewhere where your cluster nodes
and Galaxy can see it. I used the folder /opt/WoLFPSORT_package_v0.2/
meaning /opt/WoLFPSORT_package_v0.2/bin/runWolfPsortSummary
is the script itself.

Your folder ~/galaxy/CBS/WoLFPSort-master/ would be fine.

(2) Using a text editor (emacs, nano, vi, etc) create a new file named
runWolfPsortSummary (without an extension) somewhere on your
path, I suggest ~/bin/runWolfPsortSummary

$ emacs ~/bin/runWolfPsortSummary

(3) Copy this into the ~/bin/runWolfPsortSummary file,

#!/usr/bin/env python
#Wrapper script to call WoLF PSORT from its own directory.
import os
import sys
import subprocess
saved_dir = os.path.abspath(os.curdir)
os.chdir("/opt/WoLFPSORT_package_v0.2/bin")
args = ["./runWolfPsortSummary"] + sys.argv[1:]
return_code = subprocess.call(args)
os.chdir(saved_dir)
sys.exit(return_code)

(3) Mark this wrapper script as executable:

$ chmod a+x ~/bin/runWolfPsortSummary

(4) Check ~/bin is on your path, so that using runWolfPsortSummary
(without a leading dot slash) will run the new wrapper script:

$ which runWolfPsortSummary
~/bin/runWolfPsortSummary

(5) Test the new wrapper script from some other directory, e.g.

$ cd ~
$ runWolfPsortSummary animal <~/galaxy/test-data/four_human_proteins.fasta

(6) If that all works, then the Galaxy wrapper should work too.

Peter
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Re: [galaxy-dev] wolfpsort

[Olivier CLAUDE]

Ok i did not saw it.
I runned it with ./ and it worked fine. It gave me the same answer you gave me 
earlier.

Olivier

-Message d'origine-
De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : vendredi 4 décembre 2015 12:40
À : Olivier CLAUDE 
Cc : galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] wolfpsort

On Fri, Dec 4, 2015 at 11:19 AM, Olivier CLAUDE  wrote:
> Hi Peter,
> Thanks for all.
>
> ...
>
>>
>> What happens if you try to do this:
>>
>> $ cd /path/you/put/wolfpsort
>> $ ./runWolfPsortSummary animal 
>> <~/repositories/pico_galaxy/test-data/four_human_proteins.fasta
>>
>
> It gives me :
>
> olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ 
> runWolfPsortSummary animal <~/galaxy/test-data/four_human_proteins.fasta
> sh: 1: /bin/checkFastaInput.pl: not found
> sh: 1: /bin/psortModifiedForWolfFiles/psortModifiedForWoLF: not found
> /home/paulh/cbrcRepos/C++/utils/argvParsing/ArgvParser.hh:291 Error 
> opening file: "/bin/../data//animal.wolfw"
> Usage: /bin/wolfPredict [OPTIONS] weightFile trainingDataFile 
> utilityMatrixFile


That's not what I meant, there is a small but important difference.

Just runWolfPsortSummary will search the $PATH for runWolfPsortSummary script.

I wanted you to use ./runWolfPsortSummary with a dot slash at the start which 
means look in the current director for the runWolfPsortSummary script.

Please try:

$ cd ~/galaxy/CBS/WoLFPSort-master/bin
$ ./runWolfPsortSummary animal <~/galaxy/test-data/four_human_proteins.fasta

Peter


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Re: [galaxy-dev] wolfpsort

[Peter Cock]

On Fri, Dec 4, 2015 at 11:19 AM, Olivier CLAUDE  wrote:
> Hi Peter,
> Thanks for all.
>
> ...
>
>>
>> What happens if you try to do this:
>>
>> $ cd /path/you/put/wolfpsort
>> $ ./runWolfPsortSummary animal 
>> <~/repositories/pico_galaxy/test-data/four_human_proteins.fasta
>>
>
> It gives me :
>
> olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ 
> runWolfPsortSummary animal <~/galaxy/test-data/four_human_proteins.fasta
> sh: 1: /bin/checkFastaInput.pl: not found
> sh: 1: /bin/psortModifiedForWolfFiles/psortModifiedForWoLF: not found
> /home/paulh/cbrcRepos/C++/utils/argvParsing/ArgvParser.hh:291 Error 
> opening file: "/bin/../data//animal.wolfw"
> Usage: /bin/wolfPredict [OPTIONS] weightFile trainingDataFile 
> utilityMatrixFile


That's not what I meant, there is a small but important difference.

Just runWolfPsortSummary will search the $PATH for runWolfPsortSummary
script.

I wanted you to use ./runWolfPsortSummary with a dot slash at the start
which means look in the current director for the runWolfPsortSummary
script.

Please try:

$ cd ~/galaxy/CBS/WoLFPSort-master/bin
$ ./runWolfPsortSummary animal <~/galaxy/test-data/four_human_proteins.fasta

Peter
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Re: [galaxy-dev] wolfpsort

[Olivier CLAUDE]

Hi Peter,
Thanks for all.

$ arch
>x86_64

$ uname -a
>Linux LM1166 3.16.0-38-generic #52~14.04.1-Ubuntu SMP Fri May 8 
09:43:57 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

$ which perl
>/usr/bin/perl 

$ perl -v
> This is perl 5, version 18, subversion 2 (v5.18.2) built for 
x86_64-linux-gnu-thread-multi
(with 41 registered patches, see perl -V for more detail) (...)

$ /usr/bin/perl -v
> This is perl 5, version 18, subversion 2 (v5.18.2) built for 
x86_64-linux-gnu-thread-multi
(with 41 registered patches, see perl -V for more detail) (...)



NOTE: You have to pipe the input file into this tool, it does not take the 
input argument as a filename:
$ runWolfPsortSummary animal test.fasta
Command Line Parsing Error; Do not know what to do with argument "test.fasta"
Usage:
runWolfPsortSummary [*OPTIONS*] *organismType*
runWolfPsortSummary (--usage|--help|--man)
Pipe sequences in from standard in.
In your case it seems to be failing to even give this error message, apparently 
due to not finding one of the Perl files it comes with, line 37 is:

use fastafmt::GetOptWarnHandler;

Question: Where did you put the tool? Is there a .../bin/fastafmt/ folder? Is 
there are .../bin/fastafmt/GetOptWarnHandler.pm file?

I did not changed the structure of the tools as you recommanded it in 
the python script.

olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ ls
binByPlatform psortModifiedForWolfFiles  runWolfPsortSummary.py
checkFastaInput.plREADME test.fasta
fastafmt  runAddAlignmentToHtml  testQuery.fasta
GetOptWarnHandler.pm  runWolfPsortHtmlTables wolfPredict
pod   runWolfPsortSummary
WoLFPSORTpredictAndAlign

olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin/fastafmt $ ls
GetOptWarnHandler.pm

What happens if you try to do this:

$ cd /path/you/put/wolfpsort
$ ./runWolfPsortSummary animal 
<~/repositories/pico_galaxy/test-data/four_human_proteins.fasta

It gives me :

olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ runWolfPsortSummary 
animal <~/galaxy/test-data/four_human_proteins.fasta
sh: 1: /bin/checkFastaInput.pl: not found
sh: 1: /bin/psortModifiedForWolfFiles/psortModifiedForWoLF: not found
/home/paulh/cbrcRepos/C++/utils/argvParsing/ArgvParser.hh:291 Error 
opening file: "/bin/../data//animal.wolfw"
Usage: /bin/wolfPredict [OPTIONS] weightFile trainingDataFile 
utilityMatrixFile

I tried with different options :

olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ runWolfPsortSummary 
--print-neighbors animal <~/galaxy/test-data/four_human_proteins.fasta
sh: 1: /bin/checkFastaInput.pl: not found
sh: 1: /bin/psortModifiedForWolfFiles/psortModifiedForWoLF: not found
/home/paulh/cbrcRepos/C++/utils/argvParsing/ArgvParser.hh:291 Error 
opening file: "/bin/../data//animal.wolfw"
Usage: /bin/wolfPredict [OPTIONS] weightFile trainingDataFile 
utilityMatrixFile

Or

olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ runWolfPsortSummary 
--print-all-score animal <~/galaxy/test-data/four_human_proteins.fasta
Error in parsing command line. Perhaps problem with "--print-all-score"
Usage:
runWolfPsortSummary [*OPTIONS*] *organismType*

runWolfPsortSummary (--usage|--help|--man)

Pipe sequences in from standard in




Regards, 
Olivier


-Message d'origine-
De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : vendredi 4 décembre 2015 11:16
À : Olivier CLAUDE 
Cc : galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] wolfpsort

Hi Olivier,

First of all, let's double check what kind of machine you are running, in case 
that gives us some clues:

$ arch
$ uname -a

Let's double check which Perl you have,

$ which perl
$ perl -v
$ /usr/bin/perl -v

NOTE: You have to pipe the input file into this tool, it does not take the 
input argument as a filename:

$ runWolfPsortSummary animal test.fasta
Command Line Parsing Error; Do not know what to do with argument "test.fasta"
Usage:
runWolfPsortSummary [*OPTIONS*] *organismType*
runWolfPsortSummary (--usage|--help|--man)
Pipe sequences in from standard in.

In your case it seems to be failing to even give this error message, apparently 
due to not finding one of the Perl files it comes with, line 37 is:

use fastafmt::GetOptWarnHandler;

Question: Where did you put the tool? Is there a .../bin/fastafmt/ folder? Is 
there are .../bin/fastafmt/GetOptWarnHandler.pm file?

What happens if you try to do this:

$ cd /path/you/put/wolfpsort
$ ./runWolfPsortSummary
OrganismType should be one of {"fungi", "plant", "animal"}
  pipe fasta query sequences in from standard in
Usage:
runWolfPsortSummary [*OPTIONS*] *organismType*
runWolfPsortSummary (--usage|--help|--man)
Pipe sequences in from standard in.

Re: [galaxy-dev] wolfpsort

[Peter Cock]

Hi Olivier,

First of all, let's double check what kind of machine you are running,
in case that gives us some clues:

$ arch
$ uname -a

Let's double check which Perl you have,

$ which perl
$ perl -v
$ /usr/bin/perl -v

NOTE: You have to pipe the input file into this tool, it does
not take the input argument as a filename:

$ runWolfPsortSummary animal test.fasta
Command Line Parsing Error; Do not know what to do with argument "test.fasta"
Usage:
runWolfPsortSummary [*OPTIONS*] *organismType*
runWolfPsortSummary (--usage|--help|--man)
Pipe sequences in from standard in.

In your case it seems to be failing to even give this error message,
apparently due to not finding one of the Perl files it comes with,
line 37 is:

use fastafmt::GetOptWarnHandler;

Question: Where did you put the tool? Is there a .../bin/fastafmt/
folder? Is there are .../bin/fastafmt/GetOptWarnHandler.pm file?

What happens if you try to do this:

$ cd /path/you/put/wolfpsort
$ ./runWolfPsortSummary
OrganismType should be one of {"fungi", "plant", "animal"}
  pipe fasta query sequences in from standard in
Usage:
runWolfPsortSummary [*OPTIONS*] *organismType*
runWolfPsortSummary (--usage|--help|--man)
Pipe sequences in from standard in.

Or, with a real test - for example using one of the test files I often use:

$ cd /path/you/put/wolfpsort
$ ./runWolfPsortSummary animal <
~/repositories/pico_galaxy/test-data/four_human_proteins.fasta
# k used for kNN is: 32
sp|Q9BS26|ERP44_HUMAN extr 18, E.R. 5, plas 3, mito 2, lyso 2
sp|Q9NSY1|BMP2K_HUMAN nucl 25, cyto_nucl 17, cyto 7
sp|P06213|INSR_HUMAN extr_plas 11.5, plas 10.5, extr 9.5, pero 5, E.R. 4
sp|P08100|OPSD_HUMAN plas 32

Regards,

Peter

On Fri, Dec 4, 2015 at 9:13 AM, Olivier CLAUDE  wrote:
> Hello again,
>
>
>
> I cannot launch it manually neither. It gives me the same error… :
>
>
>
>>runWolfPsortSummary animal test.fasta
>
>
>
>>Can't locate fastafmt/GetOptWarnHandler.pm in @INC (you may need to install
>> the fastafmt::GetOptWarnHandler module) (@INC contains: /etc/perl
>> /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5
>> /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18
>> /usr/local/lib/site_perl . /bin) at /bin/runWolfPsortSummary line 37.
>
> BEGIN failed--compilation aborted at /bin/runWolfPsortSummary line 37.
>
>
>
> I think i missed something somewhere. Any lead?
>
>
>
> thanks
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Re: [galaxy-dev] wolfpsort

[Olivier CLAUDE]

Hello again,

 

I cannot launch it manually neither. It gives me the same error… :

 

>runWolfPsortSummary animal test.fasta

 

>Can't locate fastafmt/GetOptWarnHandler.pm in @INC (you may need to install 
>the fastafmt::GetOptWarnHandler module) (@INC contains: /etc/perl 
>/usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 
>/usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 
>/usr/local/lib/site_perl . /bin) at /bin/runWolfPsortSummary line 37.

BEGIN failed--compilation aborted at /bin/runWolfPsortSummary line 37.

 

I think i missed something somewhere. Any lead?

 

thanks

 

De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : mercredi 2 décembre 2015 18:59
À : Olivier CLAUDE 
Cc : galaxy-dev@lists.galaxyproject.org; Björn Grüning 

Objet : Re: [galaxy-dev] 3 questions

 

On Wed, Dec 2, 2015 at 5:07 PM, Olivier CLAUDE <  
o.cla...@outlook.fr> wrote:

Hello again,

 

1/

I managed to find WolfPsort on github.

 

You mean   
https://github.com/fmaguire/WoLFPSort ? I can see why Finlay Maguire did that 
although I'm not 100% sure that is within the licence.


In other news, it looks like someone else has bought the domain  
 http://wolfpsort.org/ and is holding it to random (for 
sale, offers over $1190). Oh dear. :(

 

I followed the readme file and it work with the command line but when I tried 
to run it on galaxy with the one included in the package “tmhmm and signal” 
from peterjc, it gave me an error:

 

“can’t locate fastafmt/GetOptWarnHandler.pm”

 

I put in my .bashrc the path of the file. I tried to put it directly in the 
/bin directory but it didn’t change anything.

Any idea anyone?

 

Have you followed the INSTALL file instructions? Have you been able to run 
WolfPsort at the command line?

Note it only has precompiled binaries under bin/binByPlatform for i386 and 
sparc, however we could use the 32bit binaries on our 64bit Linux machine.

 

According to my old comment inside the Python wrapper script for Galaxy, I had 
trouble running the tool from outside its home directory and so used a simple 
(second) wrapper script to change directory before running the real binary. See:

 

 
https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/wolf_psort.py#L43


 

 

 

2/in the python script I can see:

 

Num_thread = thread_count(sys.argv[2], default=4)

 

Does it means that it will use at the maximum 4 threads? Can I assume it will 
use 4 core in parallel? 

 

 

 

This means my Python wrapper script will default to 4 threads if not specified 
via the command line.

When called via Galaxy, the XML wrapper will use the $GALAXY_SLOTS environment 
variable (if set). See the job runner settings taken from job_conf.xml for 
details.

This means unless you've setup something special in Galaxy for the number of 
slots/threads to use, the tool will default to four threads. This means it will 
break up the input file into chunks and run four copies of the single threaded 
tool runWolfPsortSummary at once.


 

3/I use blast + from the devteam is there any possibility to use more than 1 
core? If yes where? 

 

 

Thanks !

 


Again, the BLAST+ wrappers will use the $GALAXY_SLOTS environment variable (if 
set), although here they default to using calling BLAST+ with 8 threads. 

 

Peter

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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

[Makis Ladoukakis]

It is uwsgi that I am trying but with apache. Could you let me know what 
changes you made to the configuration of Galaxy?

Thank you,
Makis

Date: Fri, 4 Dec 2015 10:01:56 +0200
Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed
From: p...@sanbi.ac.za
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

Hi Makis, I recently implemented something like this using uWSGI with a nginx 
frontend. Would you consider using uWSGI instead of your current approach?
On 4 Dec 2015 09:40, "Makis Ladoukakis"  wrote:



Sorry for bumping my own question but I didn't get any replies. Has anyone 
succesfully installed a production Galaxy instance? 

I could really use some advice.

Thank you,
Makis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
Date: Tue, 1 Dec 2015 18:03:44 +0200
Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed




Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]

LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so


Sethandler uwsgi-handler
uWSGISocket 127.0.0.1:4001
uWSGImaxVars 512


I am also attaching my job_conf.xml and galaxy.ini file.

  

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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Marius van den Beek]

Hello Hans,

I'm not sure if it would help to use the pre-compiled binaries,
as you would still need some of the underlying libraries for building
R packages. We're not far from having this fixed ... there is a newer
revision of R on the main toolshed,
that nevertheless will (probably) fail because of a missing include of what
seems to be fontconfig.
I had it working yesterday already, I'm trying to see what went wrong in
the meantime ...

Marius

On 4 December 2015 at 09:20, Hans Rudolph  wrote:

> Hi,
>
> I now learned that R-3.2.2 binaries for Mac OS X are available (
> https://cran.r-project.org/bin/macosx/) - could that be a potential help
> for R-related problems in galaxy on Mac OS X?
>
> Cheers,
> Hans
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,

I now learned that R-3.2.2 binaries for Mac OS X are available 
(https://cran.r-project.org/bin/macosx/) - could that be a potential help for 
R-related problems in galaxy on Mac OS X?

Cheers,
Hans
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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

[Peter van Heusden]

Hi Makis, I recently implemented something like this using uWSGI with a
nginx frontend. Would you consider using uWSGI instead of your current
approach?
On 4 Dec 2015 09:40, "Makis Ladoukakis"  wrote:

> Sorry for bumping my own question but I didn't get any replies. Has anyone
> succesfully installed a production Galaxy instance?
>
> I could really use some advice.
>
> Thank you,
> Makis
>
> --
> From: makis4e...@hotmail.com
> To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
> Date: Tue, 1 Dec 2015 18:03:44 +0200
> Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed
>
> Hello everyone,
>
> I am trying to setup a Galaxy instance for a multi-user production
> environment and I tried to follow the instructions here:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
>
> but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh
> --daemon) I got the following error in my browser:Bad Gateway The proxy
> server received an invalid response from an upstream server.
>
>
> I don't get any errors from the paster.log files so I am guessing the
> error is somewhere in my apache configuration although I can't see where it
> could be.
>
>
> Has anyone encountered this problem before?
>
> Kind regards,
> Makis
>
>
> P.S. My apache configuration is as follows:
>
> I added that to my apache httpd.conf file:
>
> #for galaxy
> #RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*)
> /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/galaxy/static/scripts/(.*)
> /home/galaxy/galaxy/static/scripts/packed/$1 [L]
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
> RewriteRule ^/galaxy/favicon.ico
> /home/galaxy/galaxy/static/favicon.ico [L]
> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt
> [L]
>
> LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so
>
> 
> Sethandler uwsgi-handler
> uWSGISocket 127.0.0.1:4001
> uWSGImaxVars 512
> 
>
> I am also attaching my job_conf.xml and galaxy.ini file.
>
>
> ___ 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
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>
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>
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