Re: [galaxy-dev] Installing dependencies from toolshed fails and produces strange folder
Thanks Dave, for letting me see the more useful stuff you can do with env.sh. Unfortunately, env.sh is not available in that tool_dependency_dir after installing the dependencies. I had my path set between quotes in the universe_wsgi.ini, producing unwanted results (the ' folder). (fe, tool_dependency_dir = '/apps'). Hence, the dependencies were installed in a place I did not want to - I moved them to the right path. BUT, no env.sh is in that folder. I cannot reinstall the dependencies via the interface neither. The quick fix I want to avoid, setting all paths hardcoded in picard tools :-/ [galaxy@galaxy e0232cbac965]$ pwd /apps/picard/1.56.0/devteam/picard/e0232cbac965 [galaxy@galaxy e0232cbac965]$ ll -alh total 12K drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 . drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 .. drwxrwxr-x 2 galaxy galaxy 4.0K Jan 8 15:07 jars I created a simple env.sh myself in that folder, but no avail. #!/bin/bash JAVA_JAR_PATH=`pwd`/jars Small question: should there not be included in the tool's xml file a statement: <requirement type="set_environment">JAVA_JAR_PATH</requirement> See http://wiki.galaxyproject.org/ToolShedToolFeatures?highlight=%28env.sh%29 Thanks, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 01/08/2013 05:53 PM, Dave Bouvier wrote:
Joachim,
JAVA_JAR_PATH is set in env.sh, which is generated during the tool dependency installation process and saved to <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/env.sh
The install code sets this variable to <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/jars
--Dave B.
*From: *Joachim Jacob <joachim.jacob@vib.be <mailto:joachim.jacob@vib.be>> *Date: *January 8, 2013 11:06:17 AM EST *To: *Greg Von Kuster <greg@bx.psu.edu <mailto:greg@bx.psu.edu>> *Subject: **Re: [galaxy-dev] Installing dependencies from toolshed fails and produces strange folder* *Reply-To: *joachim.jacob@vib.be <mailto:joachim.jacob@vib.be>
Thanks. And where is the JAVA_JAR_PATH set?
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
On 01/08/2013 04:55 PM, Greg Von Kuster wrote:
Hello Joachim,
Tool dependencies are installed into the location defined by the following entry in your universe_wsgi.ini file.
# Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies tool_dependency_dir = ../tool_dependencies
Greg Von Kuster
On Jan 8, 2013, at 10:45 AM, Joachim Jacob wrote:
Hi all,
Updating our Galaxy: the migration of some tools to the toolshed (let's take picard as an example) and installing them back from the toolshed worked well. However, during the update, I forgot to install the dependencies.
So I went to the administration part of our Galaxy, and selected 'Manage installed tool shed repositories <http://galaxy.bits.vib.be/admin_toolshed/browse_repositories>'. With the interface, I installed the dependencies for the tool (*Tool shed repository 'picard' tool dependencies*): but this failed with an error (SystemError: 1 or something alike).
After this error, I noticed a strange folder was created in the Galaxy root called '. Meaning, really called ', like "'" :-) $GALAXY_HOME/'/apps'/picard/1.56.0/devteam/picard/<revisionid>/jars
The installer installed all jars in this folder. I am currently looking into the code, but my first reflex was to think: the path is not correctly set, so heading to universe_wsgi.ini! But this seemed to be a wrong guess. Any idea what parameters are wrongly set here?
Cheers and thanks, Joachim
-- Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
___________________________________________________________ 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:
Joachim, Resolving this error will require altering database records. The steps below are for postgresql, if you're using a different database engine, the commands will be slightly different. 1. Connect to your database server, and select the database you are using for Galaxy. 2. Execute the following query: SELECT * FROM tool_dependency; 3. Find the row that has 'picard' in the name column, get the id value from that row, and execute the following query, without the <> around the id: UPDATE tool_dependency SET status='Error' WHERE id = <the id value from the previous query>; 4. Go to the page to manage the picard repository and confirm that the tool dependency shows as missing. 5. Click to review the missing tool dependency, then uninstall and reinstall the picard tool dependency. After the tool dependency installation finishes, you should find the .jar files under jars/ in the right location, and the JAVA_JAR_PATH set in env.sh. --Dave B. On 1/9/13 03:30:14.000, Joachim Jacob wrote:
Thanks Dave, for letting me see the more useful stuff you can do with env.sh. Unfortunately, env.sh is not available in that tool_dependency_dir after installing the dependencies.
I had my path set between quotes in the universe_wsgi.ini, producing unwanted results (the ' folder). (fe, tool_dependency_dir = '/apps'). Hence, the dependencies were installed in a place I did not want to - I moved them to the right path. BUT, no env.sh is in that folder. I cannot reinstall the dependencies via the interface neither. The quick fix I want to avoid, setting all paths hardcoded in picard tools :-/
[galaxy@galaxy e0232cbac965]$ pwd /apps/picard/1.56.0/devteam/picard/e0232cbac965 [galaxy@galaxy e0232cbac965]$ ll -alh total 12K drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 . drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 .. drwxrwxr-x 2 galaxy galaxy 4.0K Jan 8 15:07 jars
I created a simple env.sh myself in that folder, but no avail.
#!/bin/bash JAVA_JAR_PATH=`pwd`/jars
Small question: should there not be included in the tool's xml file a statement: <requirement type="set_environment">JAVA_JAR_PATH</requirement> See http://wiki.galaxyproject.org/ToolShedToolFeatures?highlight=%28env.sh%29
Thanks, Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
On 01/08/2013 05:53 PM, Dave Bouvier wrote:
Joachim,
JAVA_JAR_PATH is set in env.sh, which is generated during the tool dependency installation process and saved to <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/env.sh
The install code sets this variable to <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/jars
--Dave B.
*From: *Joachim Jacob <joachim.jacob@vib.be <mailto:joachim.jacob@vib.be>> *Date: *January 8, 2013 11:06:17 AM EST *To: *Greg Von Kuster <greg@bx.psu.edu <mailto:greg@bx.psu.edu>> *Subject: **Re: [galaxy-dev] Installing dependencies from toolshed fails and produces strange folder* *Reply-To: *joachim.jacob@vib.be <mailto:joachim.jacob@vib.be>
Thanks. And where is the JAVA_JAR_PATH set?
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
On 01/08/2013 04:55 PM, Greg Von Kuster wrote:
Hello Joachim,
Tool dependencies are installed into the location defined by the following entry in your universe_wsgi.ini file.
# Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies tool_dependency_dir = ../tool_dependencies
Greg Von Kuster
On Jan 8, 2013, at 10:45 AM, Joachim Jacob wrote:
Hi all,
Updating our Galaxy: the migration of some tools to the toolshed (let's take picard as an example) and installing them back from the toolshed worked well. However, during the update, I forgot to install the dependencies.
So I went to the administration part of our Galaxy, and selected 'Manage installed tool shed repositories <http://galaxy.bits.vib.be/admin_toolshed/browse_repositories>'. With the interface, I installed the dependencies for the tool (*Tool shed repository 'picard' tool dependencies*): but this failed with an error (SystemError: 1 or something alike).
After this error, I noticed a strange folder was created in the Galaxy root called '. Meaning, really called ', like "'" :-) $GALAXY_HOME/'/apps'/picard/1.56.0/devteam/picard/<revisionid>/jars
The installer installed all jars in this folder. I am currently looking into the code, but my first reflex was to think: the path is not correctly set, so heading to universe_wsgi.ini! But this seemed to be a wrong guess. Any idea what parameters are wrongly set here?
Cheers and thanks, Joachim
-- Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
___________________________________________________________ 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:
Hi Dave, Thanks for the guide. It works again. Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 01/09/2013 07:28 PM, Dave Bouvier wrote:
Joachim,
Resolving this error will require altering database records. The steps below are for postgresql, if you're using a different database engine, the commands will be slightly different.
1. Connect to your database server, and select the database you are using for Galaxy.
2. Execute the following query:
SELECT * FROM tool_dependency;
3. Find the row that has 'picard' in the name column, get the id value from that row, and execute the following query, without the <> around the id:
UPDATE tool_dependency SET status='Error' WHERE id = <the id value from the previous query>;
4. Go to the page to manage the picard repository and confirm that the tool dependency shows as missing.
5. Click to review the missing tool dependency, then uninstall and reinstall the picard tool dependency.
After the tool dependency installation finishes, you should find the .jar files under jars/ in the right location, and the JAVA_JAR_PATH set in env.sh.
--Dave B.
On 1/9/13 03:30:14.000, Joachim Jacob wrote:
Thanks Dave, for letting me see the more useful stuff you can do with env.sh. Unfortunately, env.sh is not available in that tool_dependency_dir after installing the dependencies.
I had my path set between quotes in the universe_wsgi.ini, producing unwanted results (the ' folder). (fe, tool_dependency_dir = '/apps'). Hence, the dependencies were installed in a place I did not want to - I moved them to the right path. BUT, no env.sh is in that folder. I cannot reinstall the dependencies via the interface neither. The quick fix I want to avoid, setting all paths hardcoded in picard tools :-/
[galaxy@galaxy e0232cbac965]$ pwd /apps/picard/1.56.0/devteam/picard/e0232cbac965 [galaxy@galaxy e0232cbac965]$ ll -alh total 12K drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 . drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 .. drwxrwxr-x 2 galaxy galaxy 4.0K Jan 8 15:07 jars
I created a simple env.sh myself in that folder, but no avail.
#!/bin/bash JAVA_JAR_PATH=`pwd`/jars
Small question: should there not be included in the tool's xml file a statement: <requirement type="set_environment">JAVA_JAR_PATH</requirement> See http://wiki.galaxyproject.org/ToolShedToolFeatures?highlight=%28env.sh%29
Thanks, Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
On 01/08/2013 05:53 PM, Dave Bouvier wrote:
Joachim,
JAVA_JAR_PATH is set in env.sh, which is generated during the tool dependency installation process and saved to <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/env.sh
The install code sets this variable to <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/jars
--Dave B.
*From: *Joachim Jacob <joachim.jacob@vib.be <mailto:joachim.jacob@vib.be>> *Date: *January 8, 2013 11:06:17 AM EST *To: *Greg Von Kuster <greg@bx.psu.edu <mailto:greg@bx.psu.edu>> *Subject: **Re: [galaxy-dev] Installing dependencies from toolshed fails and produces strange folder* *Reply-To: *joachim.jacob@vib.be <mailto:joachim.jacob@vib.be>
Thanks. And where is the JAVA_JAR_PATH set?
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
On 01/08/2013 04:55 PM, Greg Von Kuster wrote:
Hello Joachim,
Tool dependencies are installed into the location defined by the following entry in your universe_wsgi.ini file.
# Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies tool_dependency_dir = ../tool_dependencies
Greg Von Kuster
On Jan 8, 2013, at 10:45 AM, Joachim Jacob wrote:
Hi all,
Updating our Galaxy: the migration of some tools to the toolshed (let's take picard as an example) and installing them back from the toolshed worked well. However, during the update, I forgot to install the dependencies.
So I went to the administration part of our Galaxy, and selected 'Manage installed tool shed repositories <http://galaxy.bits.vib.be/admin_toolshed/browse_repositories>'. With the interface, I installed the dependencies for the tool (*Tool shed repository 'picard' tool dependencies*): but this failed with an error (SystemError: 1 or something alike).
After this error, I noticed a strange folder was created in the Galaxy root called '. Meaning, really called ', like "'" :-) $GALAXY_HOME/'/apps'/picard/1.56.0/devteam/picard/<revisionid>/jars
The installer installed all jars in this folder. I am currently looking into the code, but my first reflex was to think: the path is not correctly set, so heading to universe_wsgi.ini! But this seemed to be a wrong guess. Any idea what parameters are wrongly set here?
Cheers and thanks, Joachim
-- Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
___________________________________________________________ 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:
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