Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum
You'll need to white list the semi-colon which Galaxy has replaced as a security precaution (user free text can be exploited). See sanitizer here: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter Thanks: adding : sanitizer valid initial=string.printable

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 2:43 PM, John Chilton jmchil...@gmail.com wrote: Also not need to escape $__tool_directory__ (so use $__tool_directory__ instead of \$__tool_directory__). -John If this was unclear, $VAR in the command XML fragment is taken to be a Python variable available within

Re: [galaxy-dev] Importing file via FTP can silently fail, [Errno ftp error] 550

2015-02-26 Thread John Chilton
Yes - I believe it does. The top level layer (controller) is a little different because it is coming through the API - but the next 10 or so layers related to uploading are the same with the new method :). -John On Thu, Feb 26, 2015 at 9:57 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On

Re: [galaxy-dev] Importing file via FTP can silently fail, [Errno ftp error] 550

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton jmchil...@gmail.com wrote: Yeah - that is unfortunate - I agree completely that the resulting datasets should be red. I have created a Trello card here: https://trello.com/c/A6LrdjUU -John Thanks John, Does the new Download from URL or upload

Re: [galaxy-dev] problem with latest toolshed devteam cuffmerge wrapper multi-select

2015-02-26 Thread John Chilton
Is there any chance I can get you to reproduce this problem on the Galaxy test server: https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcuffcompare%2Fcuffcompare%2F2.2.1.0 and then share the history with me (jmchil...@gmail.com)? We have fixed some bugs

Re: [galaxy-dev] Importing file via FTP can silently fail, [Errno ftp error] 550

2015-02-26 Thread Nicola Soranzo
Il 26.02.2015 15:57 Peter Cock ha scritto: On Thu, Feb 26, 2015 at 2:24 PM, John Chilton wrote: Yeah - that is unfortunate - I agree completely that the resulting datasets should be red. I have created a Trello card here: https://trello.com/c/A6LrdjUU [1] -John Thanks John, Does the new

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum
On 02/26/2015 03:43 PM, John Chilton wrote: Sorry I wasn't clear about that - it hasn't reached galaxy-dist yet - you can download the latest snapshot of 15.03 release (I believe it is running on usegalaxy.org as of yesterday) via this link instead

Re: [galaxy-dev] Importing file via FTP can silently fail, [Errno ftp error] 550

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton jmchil...@gmail.com wrote: Yeah - that is unfortunate - I agree completely that the resulting datasets should be red. I have created a Trello card here: https://trello.com/c/A6LrdjUU -John I just commented on the Trello issue - as John implied

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum
On 02/26/2015 04:20 PM, John Chilton wrote: Well - this version does feature Sam's complete rewrite of the front end for tools - so things will be pretty different. Oddly though your tool loaded for me - can you open up your JavaScript console and let me know if there are any errors? my bad,

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 1:35 PM, Pierre Lindenbaum pierre.lindenb...@univ-nantes.fr wrote: You'll need to white list the semi-colon which Galaxy has replaced as a security precaution (user free text can be exploited). See sanitizer here:

Re: [galaxy-dev] Importing file via FTP can silently fail, [Errno ftp error] 550

2015-02-26 Thread John Chilton
Yeah - that is unfortunate - I agree completely that the resulting datasets should be red. I have created a Trello card here: https://trello.com/c/A6LrdjUU -John On Thu, Feb 26, 2015 at 5:19 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Feb 25, 2015 at 5:33 PM, Peter Cock

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread John Chilton
Just to make sure - since it hasn't been explicitly stated - is this tool being installed from the tool shed? The environment variable setup in tool_dependencies.xml will only be available for tool shed installs. You will also need a special requirement in your tool to make it available

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum
On 02/26/2015 02:51 PM, John Chilton wrote: Just to make sure - since it hasn't been explicitly stated - is this tool being installed from the tool shed? The environment variable setup in tool_dependencies.xml will only be available for tool shed installs. no, my future plan is to put it in

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum
Hi Peter, i wrote the tool_dependencies.xml ?xml version=1.0? tool_dependency package name=jvarkit version=1.0.0 install version=1.0.0 actions action type=set_environment environment_variable name=JVARKITDIR

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread John Chilton
Sorry I wasn't clear about that - it hasn't reached galaxy-dist yet - you can download the latest snapshot of 15.03 release (I believe it is running on usegalaxy.org as of yesterday) via this link instead https://bitbucket.org/galaxy/galaxy-central/get/release_15.03.zip. Also not need to escape

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 12:38 PM, Pierre Lindenbaum pierre.lindenb...@univ-nantes.fr wrote: Hi Peter, i wrote the tool_dependencies.xml ?xml version=1.0? tool_dependency package name=jvarkit version=1.0.0 install version=1.0.0 actions

Re: [galaxy-dev] Importing file via FTP can silently fail, [Errno ftp error] 550

2015-02-26 Thread Peter Cock
On Wed, Feb 25, 2015 at 5:33 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Using either the legacy upload tool, or the new upload widget, the following FTP URL *appears* to load into Galaxy correctly giving a green history entry. However, on closer inspection it is an empty file

[galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum
Hi Galaxy, I'm trying to put one of my java tool in galaxy. I've copied the required files in my tool directory under /tools/jvarkit (I can see it galaxy) $ ls commons-jexl-2.1.1.jar commons-logging-1.1.1.jar htsjdk-1.129.jar snappy-java-1.0.3-rc3.jar vcffilterjs.jar

[galaxy-dev] FW: Tool Testing: field inputs that occur inside repeat tag

2015-02-26 Thread Dooley, Damion
Slightly garbled there ... meant to say Help appreciated once again, Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

[galaxy-dev] Tool Testing: field inputs that occur inside repeat tag

2015-02-26 Thread Dooley, Damion
Helop aI've been testing (using planemo) some tools scheduled for toolshed publication. My first test works, but Galaxy reports that the second one fails with: Parameter %s requires a value, but has no legal values defined % self.name AssertionError: Parameter filter_column requires a value,