Re: [galaxy-dev] Redirect log files?
On Sunday, September 16, 2012, Fields, Christopher J wrote: > This seems to correspond with what I have tried; I attempter setting > log_destination in the config file (as James suggested) and the server > wouldn't start What was the error? This should work. > , but changing run.sh to point to the location worked. Not a problem, > I'll just create a modified run.sh script to not collide with hg updates. > > chris > > On Sep 12, 2012, at 2:32 PM, Nate Coraor > > wrote: > > > On Sep 12, 2012, at 1:09 PM, Fields, Christopher J wrote: > > > >> Simple question: is there a way within universe_wsgi.ini to point to a > specific location where Galaxy log (and possibly PID) files can be dropped? > I've searched for this but couldn't find an answer beyond locally > modifying run.sh, but it's entirely possible I'm missing something obvious. > >> > >> We want to have the logs stored on the server side in /var/log or > /var/spool, not on our NFS share. The way run.sh is currently grabbing > server information it seems as if we need to have something like this in > the [server:*] config section: > >> > >> [server:/var/log/galaxy/web0] > >> > >> which doesn't seem right. Maybe something like the following (per > server)? > >> > >> [server:web0] > >> use = egg:Paste#http > >> port = 8080 > >> host = 127.0.0.1 > >> use_threadpool = true > >> threadpool_workers = 7 > >> log_dir=/var/log/galaxy/ > >> > >> or simply (for all log and/or PID files): > >> > >> log_dir=/var/log/galaxy/ > > > > Hi Chris, > > > > It can't be done through the config file. You have to use the > --log-file and --pid-file from the command line. > > > > --nate > > > >> > >> chris > >> ___ > >> 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: > >> > >> http://lists.bx.psu.edu/ > > > > > ___ > 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: > > http://lists.bx.psu.edu/ > -- --jt (mobile) ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Redirect log files?
This seems to correspond with what I have tried; I attempter setting log_destination in the config file (as James suggested) and the server wouldn't start, but changing run.sh to point to the location worked. Not a problem, I'll just create a modified run.sh script to not collide with hg updates. chris On Sep 12, 2012, at 2:32 PM, Nate Coraor wrote: > On Sep 12, 2012, at 1:09 PM, Fields, Christopher J wrote: > >> Simple question: is there a way within universe_wsgi.ini to point to a >> specific location where Galaxy log (and possibly PID) files can be dropped? >> I've searched for this but couldn't find an answer beyond locally modifying >> run.sh, but it's entirely possible I'm missing something obvious. >> >> We want to have the logs stored on the server side in /var/log or >> /var/spool, not on our NFS share. The way run.sh is currently grabbing >> server information it seems as if we need to have something like this in the >> [server:*] config section: >> >> [server:/var/log/galaxy/web0] >> >> which doesn't seem right. Maybe something like the following (per server)? >> >> [server:web0] >> use = egg:Paste#http >> port = 8080 >> host = 127.0.0.1 >> use_threadpool = true >> threadpool_workers = 7 >> log_dir=/var/log/galaxy/ >> >> or simply (for all log and/or PID files): >> >> log_dir=/var/log/galaxy/ > > Hi Chris, > > It can't be done through the config file. You have to use the --log-file and > --pid-file from the command line. > > --nate > >> >> chris >> ___ >> 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: >> >> http://lists.bx.psu.edu/ > ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Return Files
Good Afternoon! I need a help. I am developing a tool in the galaxy, but I have a process that runs in the background, so that it terminates an email is sent to the user informing the end of the run, I could send the data via email, the more I need to return the data in a archive. zip to the galaxy, however only if you are not running in the background. A nice idea would be so user login or update your list of jobs I return to him the result of the execution of my tool. Hugs. -- *Alfredo Guilherme* ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] environment variables and paths for toolshed tools
Greg, Pablo,
I'm using a SnpEffect repository 'snpeff_with_dep' in
http://testtoolshed.g2.bx.psu.edu/
to test using tool_dependencies.xml with the tag.
( You both write access, if you want to use this for correcting my errors or
debugging. )
I'm getting an error in prepare_for_install:
Modulegalaxy.web.controllers.admin_toolshed:*1174*in|prepare_for_install|
|>>>|||tool_dependencies||
|{'set_environment': [{'type': 'environment variable', 'name':
'JAVA_JAR_PATH'}], 'snpEff/3.0f': {'readme': '\n', 'version': '3.0f',
'type': 'package', 'name': 'snpEff'}}|
...
Module_admin_tool_shed_repository_common_mako:*242*in|render_render_tool_dependency_section|
|>>
name*=*requirements_dict*[*'name'*]*|
*TypeError: list indices must be integers, not str*
It appears that the requirements_dict for the set_environment tag is enclosed
in an array.
I haven't yet looked at the repository code to see how that might happen.
Pablo,
The http://sourceforge.net/projects/snpeff/files/ repository should probably
have versions packaged for download named like:
http://sourceforge.net/projects/snpeff/files/snpEff_3_0.tgz
$ tar ztvf snpEff_3_0.tgz
drwxrwxrwx 0 0 0 0 Aug 23 12:17 snpEff_3_0/
-rwxrwxrwx 0 0 014298767 Aug 23 12:17 snpEff_3_0/SnpSift.jar
...
That will allow versioning within galaxy, and successive versions of
tool_dependencies.xml with only need a change to the action tag: download_by_url
Thanks,
JJ
I'm trying to test a repository that use in tool_depen
Message: 18
Date: Thu, 13 Sep 2012 11:46:32 -0400
From: Greg Von Kuster
To: David Hoover
Cc:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] environment variables and paths for toolshed
tools
Message-ID:
Content-Type: text/plain; charset="us-ascii"
Hello David,
I've just committed change set 7656:6aadac8026cb to the Galaxy central
repository that provides the ability to do what you need here. It would be
great if you could try things out and let me know if you run into any problems.
I've been working with nikhil-joshi's deseq_and_sam2counts repository in the
main Galaxy tool shed because his tools require this new feature as well. This
example should provide you with the information you'll need to tweak your tool
shed repository so that your tool dependencies are located where they get
installed rather than attempting to move them to ${GALAXY_DATA_INDEX_DIR} or
some other location.
Here is the tool_dependency.xml file entry for locating a directory referred to
by an environment variable name R_SCRIPT_PATH.
$REPOSITORY_INSTALL_DIR
The tag, is still supported inside tag sets, but
when defined at the xml root level, it will locate dependencies included in the installed
tool shed repository. Of course, the above tool_dependencies.xml file could of course also
include entries for tool dependencies that are packages, For example:
$REPOSITORY_INSTALL_DIR
http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz
./configure
--prefix=$INSTALL_DIR
make
$INSTALL_DIR/bin
You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build
R.
These tool dependency definitions are handled as described in the following
section of the tool shed wiki:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories
So in order for the dependencies to be handled when the repository is installed, they must
be defined in at least one of the tag sets in at least 1 tool config in
the repository. So, the tag set in the deseq.xml tool config file
will look something like this (there are more requirement tags defined here than in the
tool_dependencies.xml fiel above, but you should get the idea).
R_SCRIPT_PATH
R
Bioconductor
DESeq
aroma.light
lattice
The tag set in the deseq.xml tool config is also slightly altered.
Here is the way it looks before using this new approach:
stderr_wrapper.py Rscript ${GALAXY_DATA_INDEX_DIR}/deseq.R $counts $column_types
$comparison $top_table $diagnostic_html "$diagnostic_html.files_path"
"$counts.name"
To use this new feature, the command string now uses the R_SCRIPT_PATH
environment variable ( notice the required backslash to escape the $ )
stderr_wrapper.py Rscript \$R_SCRIPT_PATH/deseq.R $counts $column_types $comparison $top_table
$diagnostic_html "$diagnostic_html.files_path" "$counts.name"
When installed from the tool shed, a tool dependency object named R_SCRIPT_
