Re: [galaxy-dev] apache on ubuntu

[Will Holtz]

a2enmod adds an apache module to your list of enabled modules. Previously
enabled modules will remain enabled.

-Will

On Tue, Sep 13, 2016 at 12:10 AM, Jochen Bick 
wrote:

> Hi Will and Ray,
>
>
> > You may need to load the mod_rewrite module. This can be done via:
> > sudo a2enmod rewrite
>
> I will try that. Is this also resetting the modules of apache?
>
> >
> > -Will
> >
>
>
> >>
> >> I presume you've restarted the web server after making this change?
> >>
> >> Apache's mod_rewrite (the module you are using to achieve the above)
> >> has a logging facility, which you might want to read about:
> >>
>
> Yes I did a restart. Maybe I put the code to the wrong position?
>
> I think I will also ask somewhere else for help.
>
> Cheers Jochen
>



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Re: [galaxy-dev] apache on ubuntu

[Will Holtz]

You may need to load the mod_rewrite module. This can be done via:
sudo a2enmod rewrite

-Will

On Mon, Sep 5, 2016 at 7:10 AM, Raymond Wan  wrote:

> Hi Jochen,
>
>
>
> On Sat, Sep 3, 2016 at 2:31 AM, Bick  Jochen 
> wrote:
> > RewriteEngine on
> > RewriteRule ^(.*) http://localhost:8080$1 [P]
> ...
> > but it does not have any effect. Here the error.log but there is no
> error:
> > [Fri Sep 02 15:28:21.677881 2016] [mpm_event:notice] [pid 6627:tid
> 140049034254208] AH00493: SIGUSR1 received.  Doing graceful restart
>
> I presume you've restarted the web server after making this change?
>
> Apache's mod_rewrite (the module you are using to achieve the above)
> has a logging facility, which you might want to read about:
>
> http://httpd.apache.org/docs/current/mod/mod_rewrite.html#logging
>
> Also, as what you're trying to do isn't specific to Galaxy, you might
> want to ask your questions on other forums.  (i.e., askubuntu, etc.)
> They may not know what Galaxy is, but if you pose the problem as a
> redirection from port 80 to 8080 (and you wanted 443, as well?), I
> think an Apache expert (not me; I have gotten what you're doing
> working before, but it was a while ago and maybe I was just lucky) may
> be able to help.
>
> Ray
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Re: [galaxy-dev] Problem upgrading

[Will Holtz]

And as for "sudo git checkout v16.04" not working, it appears to me that
the release commits have not been given tags since v15.07.

-Will

On Fri, May 20, 2016 at 11:52 AM, Scott Szakonyi <scott.b.szakony...@nd.edu>
wrote:

> Will, thank you so much! That absolutely did the trick.
>
> -Scott
>
> On Fri, May 20, 2016 at 2:48 PM, Will Holtz <who...@lygos.com> wrote:
>
>> There is a 'git' missing in there. Try:
>> sudo git checkout master && git pull --ff-only origin master
>>
>> -Will
>>
>>
>> On Fri, May 20, 2016 at 11:42 AM, Scott Szakonyi <
>> scott.b.szakony...@nd.edu> wrote:
>>
>>> Hello,
>>>
>>> I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04.
>>> However, when I attempt to do so, I get an error, and git log shows I'm
>>> still on 16.01.
>>>
>>> $ sudo git checkout master && pull --ff-only origin master
>>> M tool-data/all_fasta.loc.sample
>>> Already on 'master'
>>> -bash: pull: command not found
>>>
>>>
>>> I also tried updating to the exact version:
>>>
>>> sudo git checkout v16.04
>>> error: pathspec 'v16.04' did not match any file(s) known to git.
>>>
>>>
>>> For the record, I'm using Git 1.7.1. I took my commands directory from
>>> the announcement page at
>>> https://docs.galaxyproject.org/en/master/releases/16.04_announce.html
>>>
>>> Any suggestions for ways to get the 16.04 code are greatly appreciated!
>>>
>>> Best,
>>>
>>> --
>>> Scott B. Szakonyi
>>> Research Programmer
>>>
>>> *Center for Research Computing*
>>> 107 Information Technology Center
>>> Notre Dame, IN 46556
>>> http://crc.nd.edu
>>>
>>> ___
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>>
>>
>>
>> --
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>
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>



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Re: [galaxy-dev] Problem upgrading

[Will Holtz]

There is a 'git' missing in there. Try:
sudo git checkout master && git pull --ff-only origin master

-Will


On Fri, May 20, 2016 at 11:42 AM, Scott Szakonyi 
wrote:

> Hello,
>
> I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04.
> However, when I attempt to do so, I get an error, and git log shows I'm
> still on 16.01.
>
> $ sudo git checkout master && pull --ff-only origin master
> M tool-data/all_fasta.loc.sample
> Already on 'master'
> -bash: pull: command not found
>
>
> I also tried updating to the exact version:
>
> sudo git checkout v16.04
> error: pathspec 'v16.04' did not match any file(s) known to git.
>
>
> For the record, I'm using Git 1.7.1. I took my commands directory from the
> announcement page at
> https://docs.galaxyproject.org/en/master/releases/16.04_announce.html
>
> Any suggestions for ways to get the 16.04 code are greatly appreciated!
>
> Best,
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>
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Re: [galaxy-dev] iRODS

[Will Holtz]

Please consider posting the content of your doc to the Galaxy Community Log
Board , so that other people
can find it.

-Will

On Wed, Mar 9, 2016 at 3:01 AM, Mikael Loaec <
mikael.lo...@versailles.inra.fr> wrote:

> Hi,
>
> @URGI, we have sucessfully tested connexion of galaxy instance with an
> iRODS.
> We have a pdf doc 67ko) explaining how we implement it if you want, but
> don't  know if i can send attachement on this mailinglist ?
>
> We (URGI) are also very interresting in data pull/push tools for
> Galaxy-iRODS integration. Let us know when you will begin working on it.
>
> Regards,
>
> Mikael LOAEC
> Systems and Networks Administrator
> URGI INRA
> ___
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Re: [galaxy-dev] Galaxy Startup Failing

[Will Holtz]

Hi Keith,

I use start-stop-daemon to launch python and I pass --chuid and --group to
start-stop-daemon so that galaxy does not run as root. It is my
understanding that start-stop-daemon creates the pid file as root before
changing user, as my /var/run/galaxy.pid is owned by root:root. I have
attached my /etc/init.d/galaxy script. This is from a Ubuntu 12.04 system.

-Will



On Wed, Nov 4, 2015 at 8:13 AM, Suderman Keith <suder...@cs.vassar.edu>
wrote:

> Hi Will,
>
> I tried that and it didn’t work for me.  Are you using start-stop-daemon
> to launch python?  Or do you run “python scripts/paster.py serve” from
> /etc/init.d/galaxy?
>
> If I use start-stop-daemon then python does not seem to be picking up the
> .venv.  I suspect it has something to do with .venv/bin/activate being
> sourced as root in one process and then python running as the galaxy user
> in another process.
>
> If I run “python scripts/paster.py serve” in the /etc/init.d/galaxy script
> then Galaxy is running as the root user and this is (will be) a production
> server so that is not an option.
>
> If I run python as the galaxy user from the /etc/init.d/galaxy script then
> I am back to the problem of python not being able to write to
> /var/run/galaxy.pid
>
> Keith
>
> On Nov 3, 2015, at 7:39 PM, Will Holtz <who...@lygos.com> wrote:
>
> Hi Keith,
>
> I've dealt with similar situations by adding the sourcing of
> .venv/bin/activate to the etc/init.d/galaxy script. Then none of the
> pre-existing pid code needs to be changed.
>
> -Will
>
>
> On Tue, Nov 3, 2015 at 8:55 AM, Suderman Keith <suder...@cs.vassar.edu>
> wrote:
>
>> The solution was rather simple, once I figured it out.
>>
>> The /etc/init.d/galaxy script was invoking scripts/paster.py script
>> directly so .venv/bin/activate was not being sourced.  The solution was to
>> modify /etc/init.d/galaxy to call a startup script that sourced
>> .venv/bin/activate before starting Galaxy.  I can write my solution up in
>> more detail, but now I am having some problems setting the pid file
>> correctly.
>>
>> If I use the --make-pidfile and --pidfile options for start-stop-daemon
>> in /etc/init.d/galaxy then /var/run/galaxy.pid contains the pid of the
>> startup script and not the pid of the Galaxy instance.
>>
>> If I try to set the pid in the startup script Galaxy won't start as the
>> script (now running as the Galaxy user) can't create/write the
>> /var/run/galaxy.pid file.
>>
>> My hack-around has been to touch the pid file (in case it doesn't exist)
>> and then chown it to the galaxy user in /etc/init.d/galaxy, but this
>> doesn't strike me as the correct way to do this.  Do any sysadmin gurus
>> have any better suggestions?
>>
>> Cheers,
>> Keith
>>
>> > On Nov 1, 2015, at 9:31 PM, Keith Suderman <suder...@cs.vassar.edu>
>> wrote:
>> >
>> > Greetings,
>> >
>> > I am trying to upgrade our Galaxy instance to the latest stable code
>> from master and now our instance won't start using my /etc/init.d/galaxy
>> script.  That is:
>> >
>> >> sudo service galaxy start
>> >
>> > no longer works. It says it does (i.e. prints "[OK]"), but Galaxy isn't
>> running and nothing is written to the log. I am using the init.d script
>> from simison [1], which is basically the same as the one posted to the
>> Galaxy wiki [2], both of which are quite old.
>> >
>> > Galaxy does start with:
>> >
>> >> sudo su galaxy
>> >> ./run.sh --daemon
>> >
>> > so I have left Galaxy running in a screen session for now, but that is
>> less than ideal.
>> >
>> > I suspect something to do with the .venv as `./run.sh --skip-venv` also
>> fails and I don't recall Galaxy being that finicky about a venv being
>> active. Does anyone know how I can get the /etc/init.d/galaxy script (i.e.
>> start-stop-daemon) to activate the venv for paster.py?
>> >
>> > Cheers,
>> > Keith
>> >
>> > 1. http://simison.com/brian/GalaxyAdmin_notes.html
>> > 2.
>> https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29
>> >
>> > --
>> > Research Associate
>> > Department of Computer Science
>> > Vassar College
>> > Poughkeepsie, NY
>> >
>> >
>> > ___
>> > Please keep all replies on the list by using "reply all"
>> > in your mail client.  To manage you

Re: [galaxy-dev] pbs_python can't be installed via scramble

[Will Holtz]

Hi Makis,

The thread I posted does have the exact same container.hpp error and
proposes a solution.

Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your
torque/include directory, as mentioned in that thread?

from the thread:

export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/
export PBSCONFIG=/usr/local/torque/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so


-Will


On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis 
wrote:

> Hello Will,
>
> Thank you for your reply. I had already checked this thread before as I
> browsed through the mailing list for "pbs_python" issues. It doesn't have
> the same errors (can't locate log.h and when i provide it it wants the
> container.hpp ) and up to one point i've already followed the
> "rescrambling" of the pbs_python.
>
> Anyone else had any experience with that?
>
> Thank you,
> Makis
>
> --
> Date: Tue, 22 Sep 2015 09:35:11 -0700
> Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
> From: who...@lygos.com
> To: makis4e...@hotmail.com
> CC: galaxy-dev@lists.galaxyproject.org
>
>
> Here is an old thread that looks rather similar to your problems:
>
> https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.html
>
> -Will
>
>
> On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis 
> wrote:
>
> Hello everyone,
>
> I'm trying to set up a Galaxy instance on a multi-core server in my
> university so according to the instructions here:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
>
> I installed Torque, changed the eggs.ini file by adding the 4.4.0. version
> of pbs_python
>
> and tried to setup pbs_python via scramble:
>
> LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
>
> When I did that I got the error:
>
> Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir
> via PBS_PYTHON_INCLUDEDIR variable)
> Traceback (most recent call last):
>   File "scripts/scramble.py", line 50, in 
> egg.scramble()
>   File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in
> scramble
> self.run_scramble_script()
>   File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in
> run_scramble_script
> raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % (
> sys._getframe().f_code.co_name, self.name, self.version ) )
> galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
> failed for pbs_python 4.4.0
>
> so I did some digging around and found that the file I need is in
>
> /scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
>
> (please correct me if I am wrong)
>
> So I tried again using:
>
>  
> PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
> LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
>
> but then I got the error:
>
> In file included from src/C++/pbs_ifl.h:90:0,
>  from src/C++/pbs_wrap.cxx:2978:
> /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp:
> No such file or directory
>  #include "container.hpp"
>
>
> Can someone help me please?
>
> Kind regards,
> Makis
>
>
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Re: [galaxy-dev] pbs_python can't be installed via scramble

[Will Holtz]

Here is an old thread that looks rather similar to your problems:
https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.html

-Will


On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis 
wrote:

> Hello everyone,
>
> I'm trying to set up a Galaxy instance on a multi-core server in my
> university so according to the instructions here:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
>
> I installed Torque, changed the eggs.ini file by adding the 4.4.0. version
> of pbs_python
>
> and tried to setup pbs_python via scramble:
>
> LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
>
> When I did that I got the error:
>
> Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir
> via PBS_PYTHON_INCLUDEDIR variable)
> Traceback (most recent call last):
>   File "scripts/scramble.py", line 50, in 
> egg.scramble()
>   File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in
> scramble
> self.run_scramble_script()
>   File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in
> run_scramble_script
> raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % (
> sys._getframe().f_code.co_name, self.name, self.version ) )
> galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
> failed for pbs_python 4.4.0
>
> so I did some digging around and found that the file I need is in
>
> /scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
>
> (please correct me if I am wrong)
>
> So I tried again using:
>
>  
> PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
> LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
>
> but then I got the error:
>
> In file included from src/C++/pbs_ifl.h:90:0,
>  from src/C++/pbs_wrap.cxx:2978:
> /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp:
> No such file or directory
>  #include "container.hpp"
>
>
> Can someone help me please?
>
> Kind regards,
> Makis
>
>
> ___
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Re: [galaxy-dev] galaxy.ini tool_dependency_dir change

[Will Holtz]

Yeah, that looks like it could work, or even something as simple as a
symbolic link to the new directory location should be fine.

-Will


On Wed, Sep 9, 2015 at 11:38 AM, Dooley, Damion <damion.doo...@bccdc.ca>
wrote:

> Thanks for suggestion.  I was hoping to have my tool dependencies folder
> sit alongside some other folders on a /data/ mount though.  Now after some
> searching related to your mount idea, I'm seeing "mount --bind" as a
> possible solution ... anyone use this approach?  Something like:
>
> mv /home/galaxy/tool_dependencies /data/irida/data/tool_dependencies
> mkdir /home/galaxy/tool_dependencies
> mount -o bind /data/irida/data/tool_dependencies
> /home/galaxy/tool_dependencies
>
> Regards,
>
> Damion
>
> Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre
> for Disease Control
> 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
> 
> From: Will Holtz [who...@lygos.com]
> Sent: Wednesday, September 09, 2015 11:10 AM
> To: Dooley, Damion
> Cc: galaxy-...@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] galaxy.ini tool_dependency_dir change
>
> Can you move the folder to a new drive, but mount that new drive at the
> same place within the filesystem?
>
> -Will
>



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[galaxy-dev] ldap module not present

[Will Holtz]

I'm trying out the new LDAP auth features in v15.05. I'm getting the
following error in my logs:

galaxy.auth.providers.ldap_ad DEBUG 2015-05-15 08:53:43,886 LDAP
authenticate: could not load ldap module

this is from 'import ldap' failing in lib/galaxy/auth/providers/ldap_ad.py

Should there be some egg magic that takes care of this dependency for me?

thanks,
-Will

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