from:"greg"

Hi Peter,

I've looked into this as well and again believe it is caused by a problem in 
the buildbot configuration for the main Tool Shed's Install and Test framework. 
 I've created the following Trello card for this, and we'll get it resolved 
when Dave B returns next week.

https://trello.com/c/9mLrFhTJ/209-install-and-test-framework-does-not-locate-test-data-directory-for-repositories-on-main-tool-shed

Greg Von Kuster

On May 26, 2014, at 6:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote:

 Hi guys,
 
 I just noticed two of my tools on the main ToolShed were listed under
 Latest revision: missing tool tests unexpectedly.
 
 http://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
 
 Test runs
 2014-05-25 15:12:04
Automated test environment
Tools missing tests or test data
Tool id: sample_seqs
Tool version: 0.0.1
Tool guid: 
 toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.0.1
Missing components:
Repository does not have a test-data directory.
 2014-05-13 01:43:51
Automated test environment
Tests that passed successfully
Successful installations
 2014-05-11 01:38:18
Automated test environment
Tests that passed successfully
Successful installations
 2014-05-09 01:43:58
Automated test environment
Tests that passed successfully
Successful installations
 2014-05-07 01:55:08
Automated test environment
Tests that passed successfully
Successful installations
 
 And, http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
 
 Test runs
 2014-05-25 15:10:53
Automated test environment
Tools missing tests or test data
Tool id: get_orfs_or_cdss
Tool version: 0.0.5
Tool guid: 
 toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5
Missing components:
Repository does not have a test-data directory.
 2014-05-13 05:11:12
Automated test environment
Tests that passed successfully
Successful installations
 2014-05-11 05:06:15
Automated test environment
Tests that passed successfully
Successful installations
 2014-05-09 05:17:53
Automated test environment
Tests that passed successfully
Successful installations
 2014-05-07 05:52:29
Automated test environment
Tests that passed successfully
Successful installations
 
 In both cases the most recent test run (2014-05-25) has failed in some
 way, and the ToolShed *wrongly* reports the repository does not have
 a test-data directory.
 
 Regards,
 
 Peter
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Old Tool Shed URL http://community.g2.bx.psu.edu/ dead

Hi peter,

It seems that we have stopped redirecting the old Tool Shed URL
http://community.g2.bx.psu.edu/ to the new Tool Shed URL
http://toolshed.g2.bx.psu.edu/ . I'm not sure when this happened.

Sorry for the inconvenience.

Greg Von Kuster

On May 21, 2014, at 9:37 AM, Peter Cock p.j.a.c...@googlemail.com wrote:

Hi Greg,

That Trello card link doesn't work for me, but the old domain is
currently not redirecting to the ToolShed.

Regards,

Peter

On Wed, Mar 6, 2013 at 12:32 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,

I've added this to the same Trello card. These URL redirects lie outside of
my control, so I'll bug the right person to get them set up.

https://trello.com/card/toolshed-galaxyproject-org-url-redirects/506338ce32ae458f6d15e4b3/697

Thanks!

On Mar 6, 2013, at 6:52 AM, Peter Cock wrote:

Hello all,

Either I made a typo in some old README files, or the old
URL for the Tool Shed http://community.g2.bx.psu.edu/ has
stopped working. Could this redirect to the current Tool Shed
address http://toolshed.g2.bx.psu.edu/ please?

Thanks,

Peter
___
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

___
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Old Tool Shed URL http://community.g2.bx.psu.edu/ dead

Peter, sorry, this one is out of my hands.  I'm hoping Nate can answer this 
when he gets a chance.

Greg Von Kuster

On May 27, 2014, at 11:16 AM, Peter Cock p.j.a.c...@googlemail.com wrote:

 On Tue, May 27, 2014 at 3:39 PM, Greg Von Kuster g...@bx.psu.edu wrote:
 Hi peter,
 
 It seems that we have stopped redirecting the old Tool Shed URL
 http://community.g2.bx.psu.edu/ to the new Tool Shed URL
 http://toolshed.g2.bx.psu.edu/ .  I'm not sure when this happened.
 
 Sorry for the inconvenience.
 
 Greg Von Kuster
 
 Can the old domain be restored to fix pre-existing 3rd party links?
 There could be some in published papers, certainly there are on
 the mailing list archives.
 
 Peter


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] RFC: Citations for tools

Peter, this may be the Trello card you were thinking of.

https://trello.com/c/kY7RCnd0/95-tool-shed-citation-for-tools-dois

Greg Von Kuster


On May 27, 2014, at 1:09 PM, Peter Cock p.j.a.c...@googlemail.com wrote:

 Hi Eric,
 
 I was sure there was a Trello card for this, but I can't find it right now...
 
 I've pushed this idea on the mailing list before, and in person at
 the Galaxy Community Conference too. See also these threads:
 
 http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html
 
 http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html
 
 Are you familiar enough with the area of semantic web/linked
 data to know what would be the best XML based markup to
 use for embedding the citations?
 
 i.e. We should not reinvent the wheel here ;)
 
 Peter
 
 
 On Tue, May 27, 2014 at 5:54 PM, James Taylor ja...@jamestaylor.org wrote:
 Eric, I'm very much in favor of this feature, and particularly the
 idea of generating a list of citations from a history or workflow. I
 imagine the only thing to quibble about will be the syntax. There are
 already some efforts to represent bibtex in xml (e.g.
 https://github.com/Zearin/BibTeXML), however they have always struck
 me as overly verbose.
 
 -- jt
 
 
 On Tue, May 27, 2014 at 12:45 PM, Eric Rasche rasche.e...@yandex.ru wrote:
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 I'd want to open up discussion on a feature I'd like to see. I'll try
 and implement it if I can find time this summer. I didn't see a trello
 card for anything like this yet, but please feel free to direct me there
 if I missed it.
 
 
 I'd like to see citations as a part of every tool.
 
 This would happen in the form of a citation block in the XML, which
 would contain sub-elements with text. These sub-elements could be based
 off of BibTeX, since they have existing specs for citing things:
 https://en.wikipedia.org/wiki/BibTeX
 
 These citations would then be accessible in the HTML generated tool
 pages, or via a View/Download button somewhere on the tool page. By
 storing as an XML tree, we could render these citations as BibTeX
 entries for the LaTeX users, and I believe there are ways to convert
 BibTeX to EndNote XML and so on.
 
 This could be extended for use in workflows so that when you run
 workflows, somehow a list of citations for all tools used could be
 generated.
 
 Anyone have thoughts or opinions on this?
 
 
 
 
 Using the example bibtex entry from the wikipedia page:
 
 @Book{abramowitz+stegun,
 author= Milton {Abramowitz} and Irene A. {Stegun},
 title = Handbook of Mathematical Functions with
  Formulas, Graphs, and Mathematical Tables,
 publisher = Dover,
 year  =  1964,
 address   = New York,
 edition   = ninth Dover printing, tenth GPO printing
 }
 
 I imagine it'd look like the following in a real-life tool:
 
 tool
  ...
  citation type=book
authorMilton Abramowitz and Irene A. Stegun/author
titleHandbook of Mathematical Functions with Formulas, Graphs, and
 Mathematical Tables/title
publisherDover/publisher
year1964/year
addressNew York/address
editionninth Dover printing, tenth GPO printing/edition
  /citation
 /tool
 
 
 Cheers,
 Eric
 - --
 Eric Rasche
 Programmer II
 Center for Phage Technology
 Texas AM University
 College Station, TX 77843
 404-692-2048
 e...@tamu.edu
 rasche.e...@yandex.ru
 -BEGIN PGP SIGNATURE-
 Version: GnuPG v2.0.17 (GNU/Linux)
 
 iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC
 jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU
 IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a
 FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgiogi
 0SWGIGZ6OJdqX60h2hOjJ06NhzBcTsjQea+AwTo5wAkyGPFJy4DV78jKOvsd5PMG
 qkk4U6gBcmcFolCeItlLPa/C4uiyOK2wVWHyTnEeKjdpD6dwLuemRmwtZrModbQu
 PPPFkKzQhUnh5Wgq8TIP4kSc2t1/jSpdV8MHqM0piqOFnR52fExPrwLn82WEFcp8
 tXfHHTaZj+6gL+IGswdAgqvxk1V+6QTjH57igWmYtcENpIDbhZVBh+HOD8SS2qdv
 ohwFg/Vn8VrCeTGGehNSBvkam0HXjXXq7mZ8W4xrOS8vxv8HPAFZHze2sPlUG/Ob
 WeOdiLgD2HCH95SXYDDBNFG6HwFkLETA3DjpfvgHqPdaLmEfIZW+ks1WF9RG+Pmo
 jhbWH8OmtTk5A/Zh63uRowMaDe7QSCruPIfIwlrgqLozOj8htMyJPBIW9oZGGkqC
 7Vu5UFeL8gcigRmQv5NA
 =ceAo
 -END PGP SIGNATURE-
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists

Re: [galaxy-dev] Repository installation on multiple servers

Hello Iyad and Brad,

Hello Iyad,

Yes, this is the current expected behavior.  

There is a Trllo card here that tracks progress on this issue.

http://trello.com/c/B0pV80d0/1281-messaging-and-task-queue

This work is currently in progress with a baseline implementation available in 
the upcoming Galaxy release (currently scheduled for June 2).  I'm not involved 
in this work, so I'm not quite sure whether this baseline implementation will 
handle comunication between Galaxy web front-ends like you have (and like we 
have for our public Galaxy instances), but this information should be clarified 
with the upcoming release notes.

Greg Von Kuster


On May 23, 2014, at 8:56 AM, Langhorst, Brad langho...@neb.com wrote:

 I had the same concern, and heard that this is being worked on.
 
 Meanwhile I’m using a rolling restart method from pjbriggs
 
 https://github.com/pjbriggs/galaxy-admin-utils/
 
 I’m pretty happy with this (desipite the 2 minute restart per worker) because 
 users do not see any interruption during restarts as they did before.
 
 
 Brad
 --
 Brad Langhorst, Ph.D.
 Applications and Product Development Scientist
 
 On May 23, 2014, at 8:46 AM, Kandalaft, Iyad iyad.kandal...@agr.gc.ca wrote:
 
 Hi Everyone
 
 This is my first time on the mailing list.  I am the administrator for a 
 production installation of Galaxy at Agriculture and Agri-Food Canada in 
 Ottawa, Canada.
 Currently, I have a galaxy configured to start 3 web servers and 3 handlers. 
  When installing a tool from a toolshed, only one of the three servers sees 
 the installation (the one that processed the installation request).  To 
 resolve the issue, galaxy needs to be restarted, which reloads all the tools.
 Is this the expected behaviour when a proxy server (apache) load balances 3 
 galaxy web servers?  If not, where can I start diagnosing the problem?
 
 Your assistance is much appreciated.  Thank you.
 
 Regards,
 
 Iyad Kandalaft
 Bioinformatics Programmer
 Microbial Biodiversity Bioinformatics
 Science  Technology Branch
 Agriculture  Agri-Food Canada
 iyad.kandal...@agr.gc.ca | (613) 759-1228
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] uninstalling tools via web api

Hello Evan,

When installing tools into Galaxy from the Tool Shed, you are actually 
installing Tool Shed repositories that contain tools, among other things (e.g., 
custom datatypes, exported workflows and other Galaxy utilities).  The Galaxy 
UI does provide the ability to unistall, but it is at the repository level, 
just like installing is.  You'll need to use the Manage installed tool shed 
repositories option from the Admin perspective.  The list of installed 
repositories each provide a pop-up menu to that includes options to uninstall.

Greg Von Kuster


On May 23, 2014, at 1:34 PM, Evan Bollig boll0...@umn.edu wrote:

 I notice that the galaxy web api for installing tools from the
 toolshed does not include any entrypoint for uninstalling tools. This
 must be intentional, but what was the motivation to leave this out?
 
 Cheers,
 
 -Evan Bollig
 Research Associate | Application Developer | User Support Consultant
 Minnesota Supercomputing Institute
 599 Walter Library
 612 624 1447
 e...@msi.umn.edu
 boll0...@umn.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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] new_tool_panel_section_label web api

Hello Evan,

You're referring to an object we call a ToolSectionLabel, and I don't believe 
that the Galaxy framework supports creating these objects automatically in real 
time.  You have to manually add them to one of your tool panel configs (e.g., 
tool_conf.xml, shed_tool_conf.xml, etc) via an editor.  For example, the 
label tag in the following example tool_conf.xml file will display a label 
with the text Get some data… in the Galaxy tool panel.

?xml version=1.0?
toolbox
label id=get_data text=Get some data... version= /
section id=getext name=Get Data version=
tool id=upload1 /
/section
/toolbox

Since the Galaxy framework doesn't support real time addition of section labels 
in the tool panel, the Tool Shed installation process doesn't either.  However, 
if the ability to do this is needed, we can open a Trello card for it.  Just 
let us know.

Thanks,

Greg Von Kuster


On May 23, 2014, at 1:33 PM, Evan Bollig boll0...@umn.edu wrote:

 I am using the new_tool_panel_section_label option when installing
 tools from the toolshed (via
 scripts/api/install_tool_shed_repository.py. It works, but I'm curious
 if its producing the wrong result.
 
 See the attached image. I have installed a bunch of tools with
 new_tool_panel_section_label=Other (Main Tool Shed). I see in the
 tool_conf.xml that the tool is installed under a section, and the
 section name gives the menu option its string (e.g., Other (Main Tool
 Shed)). A label on the other hand is contained within a section and
 gives a subheading string (see expected_section_and_label.png). If the
 parameter new_tool_panel_section_label specifies the section_name,
 what option exists to specify the label? Or perhaps was the *_label
 option intended to provide the subheading and another option (e.g.,
 new_tool_panel_section_name supposed to exist)?
 
 Cheers,
 
 -Evan Bollig
 Research Associate | Application Developer | User Support Consultant
 Minnesota Supercomputing Institute
 599 Walter Library
 612 624 1447
 e...@msi.umn.edu
 boll0...@umn.edu
 toolshed_installed.pngexpected_section_and_label.png___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] uninstalling tools via web api

Hi Evan,

Sorry I somehow missed that in your original message - here is a Trello card 
for enhancing the Galaxy API for the Tool Shed.  I'll get to this as soon as I 
can.

https://trello.com/c/4VktpvTd/207-enhance-the-galaxy-api-for-the-tool-shed-to-allow-uninstalling-a-repository

Greg Von Kuster

On May 23, 2014, at 2:04 PM, Evan Bollig boll0...@umn.edu wrote:

 Hey Greg,
 
 I see that option in the galaxy web UI, but I am working from the
 command line and scripting against your toolshed web api. Its the api
 that is missing the uninstall option for repositories/tools.
 
 https://wiki.galaxyproject.org/ToolShedApi
 
 Cheers,
 
 -E
 -Evan Bollig
 Research Associate | Application Developer | User Support Consultant
 Minnesota Supercomputing Institute
 599 Walter Library
 612 624 1447
 e...@msi.umn.edu
 boll0...@umn.edu
 
 
 On Fri, May 23, 2014 at 12:40 PM, Greg Von Kuster g...@bx.psu.edu wrote:
 Hello Evan,
 
 When installing tools into Galaxy from the Tool Shed, you are actually 
 installing Tool Shed repositories that contain tools, among other things 
 (e.g., custom datatypes, exported workflows and other Galaxy utilities).  
 The Galaxy UI does provide the ability to unistall, but it is at the 
 repository level, just like installing is.  You'll need to use the Manage 
 installed tool shed repositories option from the Admin perspective.  The 
 list of installed repositories each provide a pop-up menu to that includes 
 options to uninstall.
 
 Greg Von Kuster
 
 
 On May 23, 2014, at 1:34 PM, Evan Bollig boll0...@umn.edu wrote:
 
 I notice that the galaxy web api for installing tools from the
 toolshed does not include any entrypoint for uninstalling tools. This
 must be intentional, but what was the motivation to leave this out?
 
 Cheers,
 
 -Evan Bollig
 Research Associate | Application Developer | User Support Consultant
 Minnesota Supercomputing Institute
 599 Walter Library
 612 624 1447
 e...@msi.umn.edu
 boll0...@umn.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/
 
 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] TestToolShed NameError: global name 'suc' is not defined

2014-05-22 Thread Greg Von Kuster

Hi Peter,

I've been doing some refactoring in the central branch which caused this 
issuee.  It's been fixed in 13582:581e7c8e353e, which is now running on the 
test tool shed, ao this bad behavior should be resolved.

Thanks so much for reporting this.

Greg Von Kuster


On May 22, 2014, at 8:39 AM, Peter Cock p.j.a.c...@googlemail.com wrote:

 Hi all,
 
 I just hit a bug on the TestToolShed,
 
 (1) Goto http://testtoolshed.g2.bx.psu.edu/
 (2) Login
 (3) Click Latest revision: failing tool tests or similar links
 (4) Observer error page, NameError: global name 'suc' is not defined
 
 This is working on the main ToolShed.
 
 Regards,
 
 Peter
 
 --
 
 Internal Server Error
 
 Galaxy was unable to successfully complete your request
 
 URL: 
 http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositories_with_failing_tool_tests
 Module galaxy.web.framework.middleware.error:149 in __call__
 app_iter = self.application(environ, sr_checker)
 Module paste.debug.prints:106 in __call__
 environ, self.app)
 Module paste.wsgilib:543 in intercept_output
 app_iter = application(environ, replacement_start_response)
 Module paste.recursive:84 in __call__
 return self.application(environ, start_response)
 Module paste.httpexceptions:633 in __call__
 return self.application(environ, start_response)
 Module galaxy.web.framework.base:132 in __call__
 return self.handle_request( environ, start_response )
 Module galaxy.web.framework.base:190 in handle_request
 body = method( trans, **kwargs )
 Module galaxy.webapps.tool_shed.controllers.repository:239 in
 browse_my_writable_repositories_with_failing_tool_tests
 return self.my_writable_repositories_with_failing_tool_tests_grid( trans, 
 **kwd )
 Module galaxy.web.framework.helpers.grids:80 in __call__
 query = self.build_initial_query( trans, **kwargs )
 Module tool_shed.grids.repository_grids:1083 in build_initial_query
 grids_util.filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests(
  trans, repository )
 Module tool_shed.grids.util:89 in
 filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests
 repository_metadata = 
 get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, 
 repository )
 Module tool_shed.grids.util:196 in
 get_latest_downloadable_repository_metadata_if_it_includes_tools
 repository_metadata = get_latest_downloadable_repository_metadata( trans, 
 repository )
 Module tool_shed.grids.util:180 in get_latest_downloadable_repository_metadata
 latest_downloadable_revision = 
 suc.get_previous_metadata_changeset_revision( repository, repo, tip_ctx, 
 downloadable=True )
 NameError: global name 'suc' is not defined
 extra data
 
 
 full traceback
 
 text version
 This may be an intermittent problem due to load or other unpredictable
 factors, reloading the page may address the problem.
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] error: flexbar dependency is not installed by the toolshed

2014-05-20 Thread Greg Von Kuster

Hello Rui,

The problem here is that flexbar repository on the main Galaxy Tool Shed does 
not define a relationship between the flexbar tool contained within the 
repository and a recipe for installing the flexbar binary dependency.  The 
flexbar tool config includes the following requirements tag set:

requirements
requirement type=binary version=2.4flexbar/requirement
/requirements

But there is no information about how to install the flexbar binary.   The tool 
should have a a relationship to a recipt for installing the flexbar binary 
using the approach described here: 
https://wiki.galaxyproject.org/ToolsWitDependenciesInSeparateRepositories

You can contact the tool author to report this problem.  In the meantime, to 
use the tool, you'll have to install the flexbar dependency manually and make 
sure it can be found in the environment in which the tool is executed.

Greg Von Kuster


On May 19, 2014, at 10:07 PM, ruiwang.sz ruiwang...@gmail.com wrote:

 Hi Guys,
 
 I tried to install flexbar from toolshed, but upon running, error said it 
 could
 not find it.
 
 I checked and found
 
 idtoolshed.g2.bx.psu.edu/repos/jtilman/flexbar/flexbar/2.4/id
 
 in the config file, but this path does not exist.
 
 Is it that I need to install the dependency on my own? I had the impression 
 that
 toolshed will do it for me. Please correct me if I'm wrong.
 
 Thanks,
 Rui
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] The main Tool Shed is now tracking the next-stable branch in preparation for the upcoming Galaxy release

2014-05-19 Thread Greg Von Kuster

Hello all,

The upcoming Galaxy release is currently scheduled for Monday, June 2.  In 
preparation for this release, the main Galaxy Tool Shed is now tracking the 
next-stable branch and is currently running changeset 13542:11403745e7ce.  The 
main Tool Shed will be regularly updated with any additions made to the 
next-stable branch between now and the upcoming Galaxy release.

Please let us know if you encounter any issues.

Thanks very much,

Greg Von Kuster



___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] New tool listed under Latest revision: failing tool tests yet not tested

2014-05-16 Thread Greg Von Kuster

Hi Peter,

I doscovered an error in the query filters that are used for rendering these 
various Latest revision: lists.  The problem was that the filters were not 
correctly determining whether the revisions had been tested yet by the install 
and test framework.  This problem should be fixed in 13496:26b9fe985ee7, which 
is now running on the test tool shed.  Thanks for reporting this problem, and 
please let us know if you discover any other problems related to this.

Greg Von Kustet

On May 16, 2014, at 7:22 AM, Peter Cock p.j.a.c...@googlemail.com wrote:

 Hi Dave et al,
 
 Yesterday I uploaded a new tool to the TestToolShed:
 http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
 
 Development repository:
 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
 
 It is currently listed under Latest revision: failing tool tests,
 
 Name Latest Installable Revision Owner
 blast_rbh 1 (2014-05-15) peterjc
 
 On viewing the tool, there are no test results at all (yet).
 Is this a corner case false-positive, or was there really
 a failed test run which is not being shown?
 
 Thanks,
 
 Peter
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Packaging pycurl on toolshed

2014-04-29 Thread Greg Von Kuster

Hello Saket,

I'm not a system-level expert, so please ignore my attempt at helping if it is 
incorrect.  Your recipe for installing and compiling pycurl may be assuming 
that certain dependencies exist in the Galaxy environment into which it is 
being installed for testing, but they do not.  Galaxy tools and tool dependency 
recipes can only assume the following dependencies are available in the Galaxy 
environment into which they will be installed (this list is available in the 
Tool Shed wiki on this page: 
https://wiki.galaxyproject.org/InstallAndTestCertification).  In your case, a 
recipe should probably also be installing the libcurl-devel package (and 
possibly others??).

Recipes need to be created for dependencies that are not on the following list, 
and then relationships can be defined between repositories that contain them 
and repositories that contain tools that depend upon them.  The reason the 
following list is short is because starting up a new Galaxy instance should be 
as simple as cloning it and starting it up with run.sh.  

autoconf
automake
autotools-dev
build-essential
cmake
git-core
libatlas-base-dev
libblas-dev
liblapack-dev
libc6-dev
mercurial
python2.6
python2.6-dev
pkg-config
subversion
python-dev
python-pip

Greg Von Kuster


On Apr 29, 2014, at 4:34 PM, Saket Choudhary sake...@gmail.com wrote:

 Hi Bjoern,
 
 There is no script installed, I generally just do this on my local system
 $ python setup.py build --with-ssl
 $ python setup.py install
 
 The documentation mentions the following options:
 PycURL Unix options:
 --curl-config=/path/to/curl-config  use specified curl-config binary
 --openssl-dir=/path/to/openssl/dir  path to OpenSSL headers and libraries
 --with-ssl  libcurl is linked against OpenSSL
 --with-gnutls   libcurl is linked against GnuTLS
 --with-nss  libcurl is linked against NSS
 
 
 Saket
 
 On 29 April 2014 23:31, Björn Grüning bjoern.gruen...@gmail.com wrote:
 Hi Saket,
 
 is there any script installed with that package? --install-scripts may be
 needed. Also I'm wondering if there is no dependency on curl-lib?
 
 Cheers,
 Bjoern
 
 Am 29.04.2014 19:16, schrieb Saket Choudhary:
 
 Any comments on this?
 http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1
 
 On 17 April 2014 19:54, Saket Choudhary sake...@gmail.com wrote:
 
 My attempt to 'package' pycurl on testtoolshed fails with the following
 error:
 
 src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15:
 warning: call to ‘_curl_easy_getinfo_err_string’ declared with
 attribute warning: curl_easy_getinfo expects a pointer to char * for
 this info [enabled by default] src/pycurl.c: In function
 ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to
 ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning:
 curl_easy_getinfo expects a pointer to struct curl_slist * for this
 info [enabled by default] error: could not create
 '/usr/local/share/doc': Permission denied
 
 
 A local install worked fine. Is this because of libcurl-devel missing
 on toolshed instance?
 
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/
 
 
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
 

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] problem with bioc_qvalue, Version: 1.34.0

2014-04-22 Thread Greg Von Kuster

Hi Tony,

It may be easiest to just uninstall / reinstall the repository from the Manage 
installed tool shed repositories option in the admin menu.

Greg Von Kuster

On Apr 22, 2014, at 4:21 PM, Tony Kusalik kusa...@cs.usask.ca wrote:

 Thanks for the response.  I have made some progress, but I don't seem to be 
 out-of-the-woods yet.
 
 I realized that when I had invoked 
  sh ./scripts/migrate_tools/0010_tools.sh
 I had done it as root, rather than as user galaxy.  Hence I did a 
  chmod -R galaxy:galaxy
 on both the shed_tools/ and tool_dependencies/ directories.
 
 Then in the Galaxy Admin interface I selected the Installed tool shed 
 repositories option.
 I clicked on update tool shed status in the upper right corner.  I waited 
 for that update to
 complete.
 
 About 15 lines down the window is the line for compute_q_values.  It's 
 installation status was
 given as Installed, missing tool dependencies.  At the very left, it was 
 marked with a green
 check mark (This is the latest installable revision of this repository) and 
 an attention symbol
 (Updates are available in the Tool Shed for this revision).  I choose get 
 updates from the
 pull-down menu associated with compute_q_values.  The update window 
 appeared, and I toggled on
 Install.  The installation SEEMED to be okay.
 
 Now I went back to the Installed tool shed repositories window.  
 compute_q_values was marked with
 just a green check mark.  The revision column/field is given as 62f7b9c20c9b. 
  The only problem is
 that the Installation Status is still marked with Installed, missing tool 
 dependencies.
 
 Looking at the last 100 or so lines of paster.log, it appears that the 
 install of 
 compute_q_values was indeed successful.  Nothing about missing dependencies 
 reported there.
 
 Selecting update tool shed status does not change anything. 
 
 Suggestions?  Should I try running
  sh ./scripts/migrate_tools/0010_tools.sh
 again?  Or might that just make matters worse?
 
 On 2014-04-22, at 7:56 , Dave Bouvier d...@bx.psu.edu wrote:
 
 David, Tony,
 
 I have not yet been able to reproduce the behavior you've reported here. I 
 will continue to investigate, but if you go to Manage installed tool shed 
 repositories in your Galaxy admin interface and select the Update tool 
 shed status option on the compute_q_values repository, your Galaxy instance 
 should detect that there is an update available and give you the option to 
 update the repository and install its dependencies.
 
 Your report did help me uncover a potentially related issue with determining 
 dependencies of repositories that have been updated after being added to the 
 migrate_tools definition, which has now been resolved.
 
  --Dave B.
 
 On 04/17/2014 04:35 PM, David Hoover wrote:
 I saw the same phenomenon.  I think it stems from the current version of 
 compute_q_values pointing to unavailable revisions of both R and the 
 bioc_qvalue R package.  Whoever maintains the compute_q_values needs to 
 straighten out the revision ids.
 
 David Hoover
 Helix Systems Staff
 National Institutes of Health
 
 On Apr 17, 2014, at 1:38 PM, Tony Kusalik kusa...@cs.usask.ca wrote:
 
 Hi,
 
 I am having a problem with updating our local Galaxy server, and I am 
 hoping someone can help me.
 
 Yesterday I performed a 'hg incoming' command.  A bunch of updates were 
 applied, from changeset 12443:ec9d31a8bc04
 to changeset 13068:c05752549163.  I restarted the server (in daemon mode), 
 but it halted.
 The content of paster.log instructed me to run
 sh ./scripts/migrate_tools/0010_tools.sh
 I did that.  That script encountered an error:
  The following error occurred from the InstallManager while installing 
 tool dependency  bioc_qvalue :
  Error installing tool dependency package bioc_qvalue version 1.34.0: 
 Unable to locate required tool shed repository named 
 package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e.
 
 How do I get around this problem?
 
 I checked the mailing lists for anyone reporting a problem with 
 bioc_qvalue or 11735242a19e
 but nothing was turned up.
 
 Tony Kusalik
 
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
 
 
 
 ___
 Please keep all replies on the list by using reply all
 in your mail client

Re: [galaxy-dev] Using Galaxy ToolShed API for uploading a tar-ball

2014-04-10 Thread Greg Von Kuster

Hi Peter,

This is not yet available, but we'll certainly implement it.  I've created this 
Trello card for it.

https://trello.com/c/fykf8IPO/197-enhance-api-to-enable-tar-archive-uploads

Thanks!

Greg Von Kuster

On Apr 10, 2014, at 7:50 AM, Peter Cock p.j.a.c...@googlemail.com wrote:

 Hi all,
 
 I've just skimmed Greg's latest blog post which is about
 the REST API for the ToolShed:
 http://gregvonkuster.org/galaxy-tool-shed-restful-api/
 
 I would be interested in automating pushing updates to the
 ToolShed, which I currently do manually by uploading a
 tar-ball. Is it possible yet to upload a tar-ball via the API?
 
 Thanks,
 
 Peter
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Package/Module RPY

2014-04-08 Thread Greg Von Kuster

Hello Curt,

I believe that version 1.0.3 of the rpy package should be installing 
successfully from the main tool shed if you have a repository that contains a 
tool that defines a dependency to the rpy repository owned by devteam at 
http://toolshed.g2.bx.psu.edu/view/devteam/package_rpy_1_0_3
 
Here is the last test run for the tool shed's install and test framework for 
that repository.  I believe tis should install correctly using the dist 
repository, but if you're seeing problems, let us know.  Also, the next release 
is coming soon ( tentatively a week or so from now )..

Test runs  
2014-04-07 17:25:49  
Automated test environment  
Successful installations  
Repository dependencies - installation of these additional repositories is 
required  
Tool shed   NameOwner   Changeset revision
toolshed.g2.bx.psu.edu  package_r_2_11_0devteam 5824d2b3bc8b
Tool dependencies  
TypeNameVersion
R   package 2.11.0
Installation directory
/ToolDepsMain/R/2.11.0/devteam/package_rpy_1_0_3/82170c94ca7c
TypeNameVersion
rpy package 1.0.3
Installation directory
/ToolDepsMain/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c



On Apr 8, 2014, at 3:28 PM, Hayes, Curt curt.ha...@seattlechildrens.org 
wrote:

 Hi there all,
 Does anyone have RPY working? I install via toolshed and the folder is empty, 
 and shows missing dependencies.
 I have searched previous posts, nothing since 2010. I have a local install 
 (production config – postgres, etc – on CENTOS 6.5). I posted last week and 
 it fell off the list. 
 
 From Galaxy User interface:
 Dataset generation errors
 Dataset 81: Build base quality distribution on data 9
  
 Tool execution generated the following error message:
 Traceback (most recent call last):
   File 
 /apps/galaxy/galaxy-dist/tools/metag_tools/short_reads_figure_score.py, 
 line 12, in module
 from rpy import *
 ImportError: No module named rpy
  
 I have attempted to download/install the scripts but they fail with multiple 
 errors (most posts out there have a bad URL) - 
 http://getgalaxyp.org/install.html says use: 
 curlhttp://rpy.svn.sourceforge.net/viewvc/rpy/trunk/rpy/?view=tar  rpy.tar.gz
 if you view that it redirects you to another URL.  
  
 Via shell: R is installed: R version 2.13.0 (2011-04-13)
  
 Can someone provide me some help please to get it working via Galaxy? I 
 understand it works in Central.
  
 From Toolshed:
 Name
 Version
 Type
 Installation status
 rpy
 1.0.3
 package
 Error
  
 Toolshed Error:
 In file included from src/rpymodule2110.c:51: src/RPy.h:56:20: error: 
 Python.h: No such file or directory In file included from 
 /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68,
  from 
 /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, 
 from src/RPy.h:89, from src/rpymodule2110.c:51: 
 /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2:
  error: #error Must use Python with unicode enabled. truncated
 
 Thanks,
 Curt
  
 CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is 
 for the sole use of the intended recipient(s) and may contain confidential 
 and privileged information protected by law. Any unauthorized review, use, 
 disclosure or distribution is prohibited. If you are not the intended 
 recipient, please contact the sender by reply e-mail and destroy all copies 
 of the original message. 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool

2014-04-04 Thread Greg Von Kuster

Hello Björn,

I've enhanced the error message displayed in 12959:64d677b1e16a, which is
available in the next-stable branch, so it will be included in the upcoming
release. This message is tricky, because it is only displayed when visiting
the Tool Shed from Galaxy to install a repository that has an invalid
repository dependency definition. This scenario does not provide the context
for the precise cause of the invalid definition. Visiting the Tool Shed
directlry (not from Galaxy) and dispaying the repositoryu should provide a more
detailed message regarding the problem.

Thanks!

Greg Von Kuster

On Apr 3, 2014, at 10:24 AM, Björn Grüning bjoern.gruen...@gmail.com wrote:

Hi,

thanks for fixing it Greg. Would it also be possible to get a more concrete
error message in such cases where the repository_dependencies.xml file is
somehow broken?

Thanks,
Bjoern

Am 03.04.2014 16:22, schrieb Greg Von Kuster:
I should have handled the import in the same commit, but did so in the
following changeset. It will eliminate the problematic
prior_installation_required=False attribute from the repository tag when
a capsule is being imported.

changeset: 12944:59bd7349a128
tag: tip
user:greg
date:Thu Apr 03 10:19:46 2014 -0400
summary: Upon import, handle problematic prior_installation_required
attribute incorrectly added (and set to False) to the repository tag
when a repository was exported.

Greg Von Kuster

On Apr 3, 2014, at 9:53 AM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:

Thanks Greg, I will verify with new changes.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 7:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Janaki and Björn,

This problematic behavior is a result of a bug in the repository export
process which has been fixed in the following changeset which is currently
available in the Galaxy central repo. Thanks very much for reporting this.

https://bitbucket.org/galaxy/galaxy-central/commits/773578e65580e3488fadc144739d82f86d9b30f3

Greg Von Kuster

On Apr 3, 2014, at 7:53 AM, Greg Von Kuster g...@bx.psu.edu wrote:

Yes, if that is the behavior, that is definitely a bug. I'll take a look
and get back to you on this.

Thanks!

On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com
wrote:

Hi JanakiRam,

I will take Greg into CC. He is the main Tool Shed developer, maybe we
spotted a bug in populating prior_installation_required in
repository_dependencies.xml file. He probably knows if that is supposed
to work.

Greg, to summarize our findings. It seems that if JanakiRam uploads a
repository_dependencies.xml file into a local toolshed the
prior_installation_required='False' will be inserted. If he tries to
install it, Galaxy complains about a wrong syntax inside the
repository_dependecies.xml file. Imho prior_installation_required does
not make sense in repository_dependencies.xml or? Is that an bug?

JanakiRam can you confirm my summary?

Thanks,
Bjoern

Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi:
Hi,

I am using latest checkout from
https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my
local galaxy code base). Yes, without
repository dependency everything working fine.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning
bjoern.gruen...@gmail.comwrote:

Hi,

I just tested it in the test-toolshed and for me
'prior_installation_required' is not inserted. Which Galaxy version do
you
use? Please note, that I'm not sure if that is really causing the
trouble
you have seen.
If you remove the repository dependency everything is working as
expected?

Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi:

Hi Bjoern,

Please see my comments inline.

On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning
bjoern.gruen...@gmail.com
wrote:

Hi Janaki,

can you try to remove this prior_installation_required completely?

I didn't added 'prior_installation_required' in the
repository_dependencies.xml(as this is optional), it got added when I
exported repository files from tool shed. Actual
repository_dependencies.xml file has below content.

?xml version=1.0?
repositories description=test description
repository name=string_occurrence owner=janakiram-t1 /
/repositories

Also why do you need a repository dependency, I think that is not
needed
or?

This is the first time I working with repository dependencies,
so
for testing I am trying to add simple repository dependency to my
custom
tool.

Cheers,
Bjoern

Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi:

Hi Bjoern,

I also exported both the repositories from local toolshed. Please
find
the
attached files.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com

[galaxy-dev] The main Galaxy Tool Shed is now running the next-stable branch

2014-04-04 Thread Greg Von Kuster

For those interested,

The main Galaxy Tool Shed is now running the next-stable branch in preparation 
for the upcoming Galaxy release currently scheduled for about 2 weeks from now. 
 We'll continue to update the Tool Shed as new changeset are pushed to the 
next-stable branch.  We'll alert you wnen the main Tool Shed is updated to the 
stable branch when it is tagged for the next Galaxy release.

As usual, the test Galaxy Tool Shed continues to track the default branch.

Thanks!

Greg Von Kuster



___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool

2014-04-03 Thread Greg Von Kuster

Yes, if that is the behavior, that is definitely a bug.  I'll take a look and 
get back to you on this.

Thanks!

On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote:

 Hi JanakiRam,
 
 I will take Greg into CC. He is the main Tool Shed developer, maybe we 
 spotted a bug in populating prior_installation_required in 
 repository_dependencies.xml file. He probably knows if that is supposed to 
 work.
 
 Greg, to summarize our findings. It seems that if JanakiRam uploads a 
 repository_dependencies.xml file into a local toolshed the 
 prior_installation_required='False' will be inserted. If he tries to 
 install it, Galaxy complains about a wrong syntax inside the 
 repository_dependecies.xml file. Imho prior_installation_required does not 
 make sense in repository_dependencies.xml or? Is that an bug?
 
 JanakiRam can you confirm my summary?
 
 Thanks,
 Bjoern
 
 Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi:
 Hi,
 
 I am using latest checkout from
 https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my
 local galaxy code base).  Yes, without
 repository dependency everything working fine.
 
 Thanks,
 JanakiRam
 
 
 
 On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning 
 bjoern.gruen...@gmail.comwrote:
 
 Hi,
 
 I just tested it in the test-toolshed and for me
 'prior_installation_required' is not inserted. Which Galaxy version do you
 use? Please note, that I'm not sure if that is really causing the trouble
 you have seen.
 If you remove the repository dependency everything is working as expected?
 
 
 
 Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi:
 
 Hi Bjoern,
 
 Please see my comments inline.
 
 On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com
 wrote:
 
 Hi Janaki,
 
 can you try to remove this prior_installation_required completely?
 
 
I didn't added 'prior_installation_required' in the
 repository_dependencies.xml(as this is optional), it got added when I
 exported repository files from tool shed. Actual
 repository_dependencies.xml file has below content.
 
 ?xml version=1.0?
 repositories description=test description
  repository name=string_occurrence owner=janakiram-t1 /
 /repositories
 
 
 Also why do you need a repository dependency, I think that is not needed
 or?
 
 
   This is the first time I working with repository dependencies,
 so
 for testing I am trying to add simple repository dependency to my custom
 tool.
 
 
 Cheers,
 Bjoern
 
 Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi:
 
  Hi Bjoern,
 
 
 I also exported both the repositories from local toolshed. Please find
 the
 attached files.
 
 
 Thanks,
 JanakiRam
 
 
 On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi 
 janakiram.gollap...@india.semanticbits.com wrote:
 
  Hi,
 
 
 Thanks for quick reply. Please find the attached .tar file of both the
 repositories.
 
 
 Thanks,
 JanakiRam
 
 
 On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning 
 bjoern.gruen...@gmail.comwrote:
 
  This all seems to be fine, can you send me a tarball with both
 
 repositories ...
 
 Thanks,
 Bjoern
 
 Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi:
 
  Hi,
 
 
 Did anyone faced this issue ?. I struck here. Please suggest me.
 
 
 Thanks,
 JanakiRam
 
 
 On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi 
 janakiram.gollap...@india.semanticbits.com wrote:
 
   Hi,
 
 
 I have implemented a custom tool called 'barcode-parse' and uploaded
 this
 custom to into my local tool shed(which is running at
 http://localhost:9009). Also able to install this custom tool from
 galaxy.
 
 Then I have added simple repository dependency. I have created a xml
 file
 'repository_dependencies.xml'. Then I created a new repository in
 the
 toolShed called 'Test' and uploaded all necessary files(.py,
 definition
 xml
 file and repository dependency xml file) into this repository. (I
 have
 created another repository called 'string_occurrence' and uploaded
 necessary files into toolShed which is used as dependency
 repository)
 
 ?xml version=1.0?
 repositories description=
repository toolshed=http://localhost:9009;
 name=string_occurrence owner=janakiram-t1 /
 /repositories
 
 I tried to install custom tool 'barcode-parse' from galaxy, but I
 got
 below error message.
 
 The repository dependency definitions for this repository are
 invalid
 and
 will be ignored.
 
 I followed the steps mentioned in the galaxy wikihttps://wiki.
 galaxyproject.org/SimpleRepositoryDependencies
 
 
 Am I doing anything wrong? Please suggest me on this.
 
 Thanks,
 JanakiRam
 
 
 
 
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists

Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool

2014-04-03 Thread Greg Von Kuster

Hello Janaki and Björn,

This problematic behavior is a result of a bug in the repository export process
which has been fixed in the following changeset which is currently available in
the Galaxy central repo. Thanks very much for reporting this.

https://bitbucket.org/galaxy/galaxy-central/commits/773578e65580e3488fadc144739d82f86d9b30f3

Greg Von Kuster

On Apr 3, 2014, at 7:53 AM, Greg Von Kuster g...@bx.psu.edu wrote:

Yes, if that is the behavior, that is definitely a bug. I'll take a look and
get back to you on this.

Thanks!

On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote:

Hi JanakiRam,

Greg, to summarize our findings. It seems that if JanakiRam uploads a
repository_dependencies.xml file into a local toolshed the
prior_installation_required='False' will be inserted. If he tries to
install it, Galaxy complains about a wrong syntax inside the
repository_dependecies.xml file. Imho prior_installation_required does not
make sense in repository_dependencies.xml or? Is that an bug?

JanakiRam can you confirm my summary?

Thanks,
Bjoern

Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi:
Hi,

I am using latest checkout from
https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my
local galaxy code base). Yes, without
repository dependency everything working fine.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning
bjoern.gruen...@gmail.comwrote:

Hi,

I just tested it in the test-toolshed and for me
'prior_installation_required' is not inserted. Which Galaxy version do you
use? Please note, that I'm not sure if that is really causing the trouble
you have seen.
If you remove the repository dependency everything is working as expected?

Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi:

Hi Bjoern,

Please see my comments inline.

On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning bjoern.gruen...@gmail.com
wrote:

Hi Janaki,

can you try to remove this prior_installation_required completely?

?xml version=1.0?
repositories description=test description
repository name=string_occurrence owner=janakiram-t1 /
/repositories

Also why do you need a repository dependency, I think that is not needed
or?

This is the first time I working with repository dependencies,
so
for testing I am trying to add simple repository dependency to my custom
tool.

Cheers,
Bjoern

Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi:

Hi Bjoern,

I also exported both the repositories from local toolshed. Please find
the
attached files.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:

Hi,

Thanks for quick reply. Please find the attached .tar file of both the
repositories.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning
bjoern.gruen...@gmail.comwrote:

This all seems to be fine, can you send me a tarball with both

repositories ...

Thanks,
Bjoern

Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi:

Hi,

Did anyone faced this issue ?. I struck here. Please suggest me.

Thanks,
JanakiRam

On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:

Hi,

I have implemented a custom tool called 'barcode-parse' and uploaded
this
custom to into my local tool shed(which is running at
http://localhost:9009). Also able to install this custom tool from
galaxy.

Then I have added simple repository dependency. I have created a xml
file
'repository_dependencies.xml'. Then I created a new repository in
the
toolShed called 'Test' and uploaded all necessary files(.py,
definition
xml
file and repository dependency xml file) into this repository. (I
have
created another repository called 'string_occurrence' and uploaded
necessary files into toolShed which is used as dependency
repository)

?xml version=1.0?
repositories description=
repository toolshed=http://localhost:9009;
name=string_occurrence owner=janakiram-t1 /
/repositories

I tried to install custom tool 'barcode-parse' from galaxy, but I
got
below error message.

The repository dependency definitions for this repository are
invalid
and
will be ignored.

I followed the steps mentioned in the galaxy wikihttps://wiki.
galaxyproject.org/SimpleRepositoryDependencies

Am I doing anything wrong? Please suggest me

Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool

2014-04-03 Thread Greg Von Kuster

I should have handled the import in the same commit, but did so in the
following changeset. It will eliminate the problematic
prior_installation_required=False attribute from the repository tag when a
capsule is being imported.

Greg Von Kuster

On Apr 3, 2014, at 9:53 AM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:

Thanks Greg, I will verify with new changes.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 7:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Janaki and Björn,

https://bitbucket.org/galaxy/galaxy-central/commits/773578e65580e3488fadc144739d82f86d9b30f3

Greg Von Kuster

On Apr 3, 2014, at 7:53 AM, Greg Von Kuster g...@bx.psu.edu wrote:

Yes, if that is the behavior, that is definitely a bug. I'll take a look
and get back to you on this.

Thanks!

On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote:

Hi JanakiRam,

JanakiRam can you confirm my summary?

Thanks,
Bjoern

Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi:
Hi,

I am using latest checkout from
https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my
local galaxy code base). Yes, without
repository dependency everything working fine.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning
bjoern.gruen...@gmail.comwrote:

Hi,

I just tested it in the test-toolshed and for me
'prior_installation_required' is not inserted. Which Galaxy version do
you
use? Please note, that I'm not sure if that is really causing the trouble
you have seen.
If you remove the repository dependency everything is working as
expected?

Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi:

Hi Bjoern,

Please see my comments inline.

On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning
bjoern.gruen...@gmail.com
wrote:

Hi Janaki,

can you try to remove this prior_installation_required completely?

?xml version=1.0?
repositories description=test description
repository name=string_occurrence owner=janakiram-t1 /
/repositories

Also why do you need a repository dependency, I think that is not needed
or?

This is the first time I working with repository dependencies,
so
for testing I am trying to add simple repository dependency to my custom
tool.

Cheers,
Bjoern

Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi:

Hi Bjoern,

I also exported both the repositories from local toolshed. Please find
the
attached files.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:

Hi,

Thanks for quick reply. Please find the attached .tar file of both
the
repositories.

Thanks,
JanakiRam

On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning
bjoern.gruen...@gmail.comwrote:

This all seems to be fine, can you send me a tarball with both

repositories ...

Thanks,
Bjoern

Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi:

Hi,

Did anyone faced this issue ?. I struck here. Please suggest me.

Thanks,
JanakiRam

On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:

Hi,

I have implemented a custom tool called 'barcode-parse' and
uploaded
this
custom to into my local tool shed(which is running at
http://localhost:9009). Also able to install this custom tool from
galaxy.

Then I have added simple repository dependency

Re: [galaxy-dev] How to write test cases for custom tool

2014-03-27 Thread Greg Von Kuster

As Janaki replied below, see:
http://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests

On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:

Hi,

I have added tests to tool dependency xml, but how should I run these tests,
can you please help me to run test cases.

.
tests
test
param name=input1 value=some string/
param name=input2 value=expected format/
output name=output file=output.txt/
/test
/tests
..

Thanks,
G.JanakiRam

On Thu, Mar 27, 2014 at 3:27 PM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:
Hi,

I found below resources:
Running test
Writing Functional tests

Thanks,
JanakiRam

On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama Rao Gollapudi
janakiram.gollap...@india.semanticbits.com wrote:
Hi,

I have implemented a custom tool which will parse a given string in to
expected format. Installed this custom tool into galaxy and was able to run
successfully.

I would like to add test cases to this tool, can you please provide me
resources to write test cases for this custom tool.

Is this tool need functional, unit, integration test cases ? I am not sure
about which test cases needed for this tool.

Thanks,
JanakiRam

___
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

___
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] How to write test cases for custom tool

2014-03-27 Thread Greg Von Kuster

Hello Janaki,

Thanks for clarifying that you have installed your tools from a Tool Shed.  In 
this case, functional tests do not use Galaxy's tool_conf.xml.sample, so 
changing it will make no difference.  For information about running functional 
tests on tools installed from the Tool Shed, see: 
https://wiki.galaxyproject.org/TestingInstalledTools

Basically, you'll be doing the following.  The functional test framework is not 
currently set up to test a specific installed tool using a -id flag.  You'll 
have to use just the -installed flagg which will end up testing all installed 
tools.

export GALAXY_TOOL_DEPENDENCY_DIR=tool_dependencies;  sh 
run_functional_tests.sh -installed

Greg Von Kuster

On Mar 27, 2014, at 8:58 AM, Janaki Rama Rao Gollapudi 
janakiram.gollap...@india.semanticbits.com wrote:

 Hi,
 
 Thanks for reply. I composed a details email for better clarity. 
 
 when run grep command in galaxy home folder ( ./run_functional_tests.sh -list 
 | grep barcode-parse), I got no results. 
 What I did was:
 Implemented a custom tool (It has one python script and tool definition file. 
 These files are located in ../tools/Mytools/customToolName/)
 Then run the ToolShed in my local which is running on port 9009 (I have)
 Created a new repository in the ToolShed (which is running on 9009) and 
 uploaded .py and .xml files in to it
 Now I run the galaxy (running on port 8080) and browse the my custom tool 
 from my local galaxy and install the custom tool successfully
 And shed_tool_conf.xml file updated with new section: 
 section id=mTools name=MyTools version=
   tool 
 file=xxx.xx.x.xx/repos/janakiram-t1/barcode_parse_1/b6a60d02b1a2/barcode_parse_1/barcode-
   parse.xml 
 guid=xxx.xx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0
   tool_shedxxx.xxx.x.xx:9009/tool_shed
 repository_namebarcode_parse_1/repository_name
 repository_ownerjanakiram-t1/repository_owner
 
 installed_changeset_revisionb6a60d02b1a2/installed_changeset_revision
 
 idxxx.xxx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0/id
 version1.0.0/version
 /tool
 /section
 
 My tool definition  file look likes below:
 tool id=barcode-parse name=Barcode parse
 descriptionsome description/description
 command interpreter=pythonbarcode-parse.py $input1 $input2 
 $output/command
 inputs
 param format=input name=input1 type=text size=50 
 label=barcode help=Enter barcode
validator type=empty_field message=please enter 
 barcode/
   /param
   param format=input name=input2 type=text size=50 
 label=Expected format help=Enter format to parse barcode
   validator type=empty_field message=please enter 
 expected format barcode/ 
   /param
 /inputs
 outputs
 data format=txt name=output /  
 /outputs
 tests
test
  param name=input1 
 value=test-01-sample-test-02-sampl1-test-03-sample3/
  param name=input2 value=name-id/
  output name=output file=barcode-parse.txt/
/test
 /tests
 help
Parse the barcode into expected format
 /help
 /tool
 As galaxy using  tool_conf.xml.sample, this file has no section for my custom 
 tool. I have added a section manually like below:
 
  section name=MyTools id=mTools
  tool file=myTools/barcode-parse/barcode-parse.xml /
   /section
 
 Then my tool id found when I run the grep command. After that Then I run the 
 below command to run the test cases:
 
 sh run_functional_tests.sh -id barcode-parse
 
 But I got below out put (from the run_functional_tests.html)
 
 
 AttributeError: 'module' object has no attribute 
 'test_toolbox:TestForTool_barcode-parse'
 
 Am I doing anything wrong.
 
 Thanks,
 JanakiRam
 
 
 On Thu, Mar 27, 2014 at 6:16 PM, Greg Von Kuster g...@bx.psu.edu wrote:
 As Janaki replied below, see: 
 http://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests
 
 On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi 
 janakiram.gollap...@india.semanticbits.com wrote:
 
 Hi,
 
 I have added tests to tool dependency xml, but how should I run these tests, 
 can you please help me to run test cases. 
 
 .
  tests
test
  param name=input1 value=some string/
  param name=input2 value=expected format/
  output name=output file=output.txt/
/test
 /tests
 ..
 
 
 Thanks,
 G.JanakiRam
 
 
 
 
 On Thu, Mar 27, 2014 at 3:27 PM, Janaki Rama Rao Gollapudi 
 janakiram.gollap...@india.semanticbits.com wrote:
 Hi,
 
 I found below resources:
  Running test
 Writing Functional tests
 
 Thanks,
 JanakiRam
 
 
 On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama Rao Gollapudi 
 janakiram.gollap...@india.semanticbits.com wrote:
 Hi,
 
 I have implemented a custom tool which will parse a given string in to 
 expected format

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

2014-03-26 Thread Greg Von Kuster

Hi Geert,

The setting should be in your universe_wsgi.ini.sample, and you woud have to 
manually edit your universe_wsgi.ini to add it.  I would say that 125 installed 
packages is probably what is causing the slow starts.  This feature is not 
currently useful, so it can be set to not function with no problems.  In the 
future I'll introduce additional benefits for this feature, and I'll look at 
ways to improve the startup speed.

Greg Von Kuster

On Mar 26, 2014, at 3:43 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be 
wrote:

 hi Greg, 
 
 I don't have that setting in my universe. Should I just add it? The output of 
 hg summary is (hg incoming doesn't show any available updates): 
 
 parent: 12276:dc067a95261d tip
  Added tag release_2014.02.10 for changeset 5e605ed6069f
 branch: stable
 commit: 22 modified, 1 deleted, 127 unknown
 update: (current)
 
 I currently have 125 packages from toolsheds. Is that considered to be 
 many? Most of them are the migrated tools and the devteam 
 mappers/gatk/tophat stuff. 
 
 Geert
 
 
 
 On 03/25/2014 05:16 PM, Greg Von Kuster wrote:
 Hello Geert,
 
 Do you have a lot of repositories installed from the Tool Shed into you 
 Galaxy instance?  if so, the time you're experience may be due to loading 
 the in-memory installed repository registry.  Using this registry is 
 optional, but the default configuration setting is to use it.  You can set 
 the following to entry to False in your universe_wsgi.ini file and restart 
 your Galaxy server to see if that is the problem.  This registry is not 
 currently used by anythin except to display the set of dependent 
 repositories that will be affected if a repository is uninstalled.  If this 
 is ot what is causing the slow statup, then I'm not sure where else to look.
 
 # Enable use of an in-memory registry with bi-directional relationships
 # between repositories (i.e., in addition to lists of dependencies for a
 # repository, keep an in-memory registry of dependent items for each 
 repository.
 #manage_dependency_relationships = True
 
 Greg Von Kuster
 
 
 On Mar 25, 2014, at 11:08 AM, Geert Vandeweyer 
 geert.vandewey...@uantwerpen.be wrote:
 
 
 Dear all,
 
 I'm wondering if the following behaviour is normal. Since I reinstalled the 
 latest galaxy distribution, every restart hangs/loads for up to 10 minutes 
 at the following lines:
 
 galaxy.model.migrate.check INFO 2014-03-25 15:56:57,965 At database version 
 118
 tool_shed.galaxy_install.migrate.check INFO 2014-03-25 15:56:58,477 At 
 migrate_tools version 9
 galaxy.config INFO 2014-03-25 15:56:58,694 Install database targetting 
 Galaxy's database configuration.
 
 
 After several minutes of no heavy processing (cpu/database is almost idle), 
 the startup continues.
 
 Best,
 
 Geert
 
 -- 
 
 Geert Vandeweyer, Ph.D.
 Department of Medical Genetics
 University of Antwerp
 Prins Boudewijnlaan 43
 2650 Edegem
 Belgium
 Tel: +32 (0)3 275 97 56
 E-mail: geert.vandewe...@ua.ac.be
 http://ua.ac.be/cognitivegenetics
 http://www.linkedin.com/in/geertvandeweyer
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 
 
 
 -- 
 
 Geert Vandeweyer, Ph.D.
 Department of Medical Genetics
 University of Antwerp
 Prins Boudewijnlaan 43
 2650 Edegem
 Belgium
 Tel: +32 (0)3 275 97 56
 E-mail: geert.vandewe...@ua.ac.be
 http://ua.ac.be/cognitivegenetics
 http://www.linkedin.com/in/geertvandeweyer

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

2014-03-26 Thread Greg Von Kuster

The changeset that made this a configurable setting was committed to the stable 
branch in d270d3c, which was committed on 2014-02-19

https://bitbucket.org/galaxy/galaxy-central/commits/d270d3cf7627a42b6fac2aa69701deadb89c8ffc

If you are tracking the stable branch in the galaxy central repo (which it 
looks like you are doing), then you should be able to pull it from there.

Greg Von Kuster

On Mar 26, 2014, at 8:04 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be 
wrote:

 Hi Greg, 
 
 The setting was not in my universe_sample file. I added it, set log_info to 
 DEBUG and restarted galaxy. 
 
 The startup time remained the same, and there were many entries in the log 
 file indicating that the lag is indeed the creation of the dependency system: 
 
 
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:01,176 Adding an entry for version 0.1.18 of package samtools to 
 runtime_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:02,645 Adding an entry for version 0.1.18 of package samtools to 
 installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:03,874 Adding an entry for version 0.1.18 of package samtools to 
 runtime_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:05,383 Adding an entry for version 0.1.18 of package samtools to 
 installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:06,533 Adding an entry for version 2.11.0 of package R to 
 runtime_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:08,054 Adding an entry for version 2.11.0 of package R to 
 installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:09,126 Adding an entry for version 2.11.0 of package R to 
 runtime_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:10,596 Adding an entry for version 2.11.0 of package R to 
 installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:11,803 Adding an entry for version 1.02.00 of package lastz to 
 runtime_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:13,332 Adding an entry for version 1.02.00 of package lastz to 
 installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:14,552 Adding an entry for version 3.0.1 of package R_3_0_1 to 
 runtime_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:15,943 Adding an entry for version 3.0.1 of package R_3_0_1 to 
 installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:17,162 Adding an entry for version 0.1.18 of package samtools to 
 runtime_tool_dependencies_of_installed_tool_dependencies.
 tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-03-26 
 13:01:18,594 Adding an entry for version 0.1.18 of package samtools to 
 installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
 etc...
 
 I also note many double entries in the log files. 
 
 Do I need a specific changeset for the parameter setting to take effect? 
 
 Universe_wsgi.ini setting: 
  
 # Enable use of an in-memory registry with bi-directional relationships 
 between repositories
 manage_dependency_relationships = False
 
 Best, 
 
 Geert
 
 
 On 03/26/2014 11:53 AM, Greg Von Kuster wrote:
 Hi Geert,
 
 The setting should be in your universe_wsgi.ini.sample, and you woud have to 
 manually edit your universe_wsgi.ini to add it.  I would say that 125 
 installed packages is probably what is causing the slow starts.  This 
 feature is not currently useful, so it can be set to not function with no 
 problems.  In the future I'll introduce additional benefits for this 
 feature, and I'll look at ways to improve the startup speed.
 
 Greg Von Kuster
 
 On Mar 26, 2014, at 3:43 AM, Geert Vandeweyer 
 geert.vandewey...@uantwerpen.be wrote:
 
 hi Greg, 
 
 I don't have that setting in my universe. Should I just add it? The output 
 of hg summary is (hg incoming doesn't show any available updates): 
 
 parent: 12276:dc067a95261d tip
  Added tag release_2014.02.10 for changeset 5e605ed6069f
 branch: stable
 commit: 22 modified, 1 deleted, 127 unknown
 update

Re: [galaxy-dev] prims workflows

2014-03-25 Thread Greg Von Kuster

Hello Pieter,

When you install a repository into Galaxy that contains workflows, you can 
import the workflow into Galaxy.  At the time the workflow is imported, the 
import process checks to see if all required tools are available in Galaxy.  If 
not, a page is displayed with links to accessible Tool Sheds allowing the user 
to search for missing required tools.  I believe this still works, although 
there have been some changes to the workflow framework over the past several 
months, and I have not checked to see if this is still available.  See 
https://wiki.galaxyproject.org/ToolShedWorkflowSharing for more details.  

This approach is basically a hack that I implemented several years ago.  A 
much better approach would be to enhance the workflow UI to include a feature 
allowing the user to search Tool Sheds to discover and install missing tools 
required by any workflow currently abvailable in the Galaxy instance.  
Hopefully at some point soon something like this will be introduced.

Greg Von Kuster

On Mar 25, 2014, at 6:47 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote:

 Hi Bjoern,
 
 I think you may have misunderstood me. What I mean is : instead of me having 
 to add a tool_dependencies or repository_dependencies.xml to the workflows 
 package, let Galaxy Tool Shed find these dependencies based on metadata 
 available in the workflow itself. 
 
 Best regards,
 
 Pieter.
 
 -Original Message-
 From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] 
 Sent: dinsdag 25 maart 2014 11:43
 To: Lukasse, Pieter; Greg Von Kuster (g...@bx.psu.edu)
 Subject: Re: FW: prims workflows
 
 Hi Pieter,
 
 if I'm not misunderstood you, thats already possible:
 
 Have a look at:
 https://github.com/bgruening/galaxytools/tree/master/workflows/glimmer3
 
 For an example.
 Cheers,
 Bjoern
 
 Am 25.03.2014 11:08, schrieb Lukasse, Pieter:
 Hi Greg,
 
 Do you have any plans of resolving the dependencies automatically when it 
 comes to workflows? E.g. I have a Tool Shed repository where I would like to 
 add workflows that are constructed using tools from different repositories. 
 It would be nice if you could let Tool Shed install the tools automatically 
 upon installation of the workflow. Any plans?
 
 Best regards,
 
 Pieter
 
 -Original Message-
 From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
 Sent: zaterdag 22 maart 2014 16:25
 To: Lukasse, Pieter
 Subject: prims workflows
 
 Hi Pieter,
 
 thanks for your prims Galaxy contributions.
 Any chance to add a repository_dependencies.xml file to the workflow 
 repository?
 
 Thanks,
 Bjoern
 
 
 
 
 


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] tophat2 install

2014-03-25 Thread Greg Von Kuster

If you installe dit from the main Tool Shed, then this repository has the 
recipe for installing the package.

http://toolshed.g2.bx.psu.edu/view/devteam/package_tophat2_2_0_9 

Greg Von Kuster
 
On Mar 25, 2014, at 9:25 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
wrote:

 Hi,
 
 Not sure if you saw my last email. Updating to the latest patch version 
 doesn't seem to help.  I was wondering where I could get the galaxy package 
 version of tophat2 and put it where it needs to be manually.  Then I could 
 try the uninstall/install and see if that helps.
 
 Thanks!
 -Sheldon
 
 -Original Message-
 From: galaxy-dev-boun...@lists.bx.psu.edu 
 [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
 Sent: Thursday, March 20, 2014 3:11 PM
 To: 'Greg Von Kuster'
 Cc: galaxy-dev@lists.bx.psu.edu Dev
 Subject: Re: [galaxy-dev] tophat2 install
 
 No difference.  Same error
 
 -Original Message-
 From: Greg Von Kuster [mailto:g...@bx.psu.edu]
 Sent: Thursday, March 20, 2014 2:56 PM
 To: Briand, Sheldon
 Cc: galaxy-dev@lists.bx.psu.edu Dev
 Subject: Re: [galaxy-dev] tophat2 install
 
 Sorry, should have advised this:
 
 hg pull https://bitbucket.org/galaxy/galaxy-central#stable
 hg update stable
 
 See the end ot this thread:
 
 http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-td4663719.html
 
 
 
 
 On Mar 20, 2014, at 1:51 PM, Björn Grüning bjoern.gruen...@gmail.com wrote:
 
 Hi,
 
 you need to track galaxy-central to make use of the patches that are applied 
 as bugfixes after the release. You can do that easily with changing the path 
 in .hg/hgrc ... but I do not know if that is the right way to do ;) For me 
 it worked.
 
 Cheers,
 Bjoern
 
 Am 20.03.2014 18:46, schrieb Briand, Sheldon:
 pulling from https://bitbucket.org/galaxy/galaxy-dist
 searching for changes
 no changes found
 
 From: Greg Von Kuster [mailto:g...@bx.psu.edu]
 Sent: Thursday, March 20, 2014 2:36 PM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
 
 There have been several fixes released to the stable branch that you do not 
 have in 12441.  I would recommend doing the following:
 
 hg pull
 hg update stable
 
 Then uninstall the tophat2 repository and reinstall it.  See if that makes 
 a difference.
 
 
 On Mar 20, 2014, at 1:30 PM, Briand, Sheldon 
 sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote:
 
 
 $ hg summary
 parent: 12441:dc067a95261d
 
 From the tool_dependencies.xml:
 
 package name=tophat2 version=2.0.9
  repository changeset_revision=8549fd545473 
 name=package_tophat2_2_0_9 owner=devteam 
 prior_installation_required=False toolshed 
 =http://toolshed.g2.bx.psu.edu; /
 
 
 From: Greg Von Kuster [mailto:g...@bx.psu.eduhttp://bx.psu.edu]
 Sent: Thursday, March 20, 2014 2:23 PM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
 
 What version of Galaxy are you running?  You want to look in the tophat2 
 repository directory, not its package dependency.  There should be a 
 tool_dependencies.xml file in the tophat2's installation directory 
 hierarchy somewhere.
 
 On Mar 20, 2014, at 1:12 PM, Briand, Sheldon 
 sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote:
 
 
 
 Hi,
 
 dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
 contains only:
 env.sh
 
 If that isn't the right place to look let me know.
 
 -Sheldon
 
 From: Greg Von Kuster [mailto:g...@bx.psu.eduhttp://bx.psu.edu]
 Sent: Thursday, March 20, 2014 2:04 PM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
 
 It looks like your database and file system are out of sync.  Your database 
 seems to think you have an installed repository but your file system does 
 not seem to have the repository's installation directory.  Can you confirm 
 that this is the case?
 
 
 On Mar 20, 2014, at 11:53 AM, Briand, Sheldon 
 sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote:
 
 
 
 
 Hi,
 
 Here is the error from the paster.log:
 
 Traceback (most recent call last):
  File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py, 
 line 496, in handle_tool_dependencies
from_install_manager=from_install_manager )
  File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 318, in install_package
from_install_manager=from_install_manager )
  File
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 245, in handle_complex_repository_d ependency_for_package
tool_dependencies_config = get_absolute_path_to_file_in_repository( 
 repo_files_dir, 'tool_dependencies.xml' )
  File
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

2014-03-25 Thread Greg Von Kuster

Hello Geert,

Do you have a lot of repositories installed from the Tool Shed into you Galaxy 
instance?  if so, the time you're experience may be due to loading the 
in-memory installed repository registry.  Using this registry is optional, but 
the default configuration setting is to use it.  You can set the following to 
entry to False in your universe_wsgi.ini file and restart your Galaxy server to 
see if that is the problem.  This registry is not currently used by anythin 
except to display the set of dependent repositories that will be affected if a 
repository is uninstalled.  If this is ot what is causing the slow statup, then 
I'm not sure where else to look.

# Enable use of an in-memory registry with bi-directional relationships
# between repositories (i.e., in addition to lists of dependencies for a
# repository, keep an in-memory registry of dependent items for each repository.
#manage_dependency_relationships = True

Greg Von Kuster


On Mar 25, 2014, at 11:08 AM, Geert Vandeweyer 
geert.vandewey...@uantwerpen.be wrote:

 
 Dear all,
 
 I'm wondering if the following behaviour is normal. Since I reinstalled the 
 latest galaxy distribution, every restart hangs/loads for up to 10 minutes at 
 the following lines:
 
 galaxy.model.migrate.check INFO 2014-03-25 15:56:57,965 At database version 
 118
 tool_shed.galaxy_install.migrate.check INFO 2014-03-25 15:56:58,477 At 
 migrate_tools version 9
 galaxy.config INFO 2014-03-25 15:56:58,694 Install database targetting 
 Galaxy's database configuration.
 
 
 After several minutes of no heavy processing (cpu/database is almost idle), 
 the startup continues.
 
 Best,
 
 Geert
 
 -- 
 
 Geert Vandeweyer, Ph.D.
 Department of Medical Genetics
 University of Antwerp
 Prins Boudewijnlaan 43
 2650 Edegem
 Belgium
 Tel: +32 (0)3 275 97 56
 E-mail: geert.vandewe...@ua.ac.be
 http://ua.ac.be/cognitivegenetics
 http://www.linkedin.com/in/geertvandeweyer
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] tool_dependencies.xml Environmental Variable Question

2014-03-24 Thread Greg Von Kuster

Hello Michael,

Environment variables properly defined in a tool's associated 
tool_dependencies.xml file contained in an installed Tool Shed repository 
should be available to the tool's environment at runtime.  Do you have an 
example where you are not seeing this?

Greg Von Kuster

On Mar 21, 2014, at 1:22 PM, Michael E. Cotterell mepcotter...@gmail.com 
wrote:

 Is the expected behavior that environmental variables setup in a tool’s 
 tool_dependencies.xml file are not available in the tool’s python virtualenv 
 during runtime? It’s seems odd that we can specify modules (installable from 
 pip) that are available during runtime, but that the environmental variables 
 are not available during runtime.  
 
 Thanks!  
 
 Sincerely,
 Michael E. Cotterell
 
 Ph.D. Student in Computer Science, University of Georgia
 Instructor of Record, Graduate RA  TA, University of Georgia
 Department Liaison, CS Graduate Student Association, University of Georgia
 mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
 mepc...@uga.edu (mailto:mepc...@uga.edu)
 m...@cs.uga.edu (mailto:m...@cs.uga.edu)
 http://michaelcotterell.com/
 
 
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
 


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] tophat2 install

Hi Sheldon,

I recommend not manually changing any database entries.  You should be able to 
install the repository and all of its dependencies using the Repair Repository 
feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories

Greg Von Kuster

On Mar 20, 2014, at 8:59 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
wrote:

 Hi,
  
 Just wondering if I can still use the following to fix up my messed up 
 tophat2 install (the install had hung up on me, for 2 hours, and I tried to 
 remove/repair it via the interface).  I haven’t had problems installing any 
 other tools or packages.  I am using postgres but this advice was given 2 
 years ago to another user and fields may have changed.  Thanks for any help!
 -Sheldon  
  
 1. Manually remove the installed repository subdirectory hierarchy from disk. 
 2. If the repository included any tools, manually remove entries for each of 
 them from the shed_tool-conf.xml file ( or the equivalent file you have 
 configured for handling installed repositories ) 
 3. Manually update the database using the following command (assuming your 
 installed repository is named 'bcftools_view' and it is the only repository 
 you have installed with that name) - letter capitalization is required: 
 
 The following assumes you're using postgres: 
 
 update tool_shed_repository set deleted=True, uninstalled=True, 
 status='Uninstalled', error_message=Null  where name = 'bcftools_view';
  
  
  
 From: Briand, Sheldon 
 Sent: Wednesday, March 12, 2014 11:44 AM
 To: galaxy-dev@lists.bx.psu.edu
 Subject: tophat2 install
  
 Hi,
  
 I ran into a problem installing tophat2 here:
 tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType 
 found
  
 I have only used the interface to do the installation (no manual deletes).  
 The rest of the dependencies for tophat2 installed just fine.
  
 Repairing the repository doesn’t make any difference.
  
 Thanks!
 -Sheldon
  
 Sheldon Briand
 NRC Research Computing Support Analyst
 Research Computing Support / Soutien Informartique a la Recherche
 Operations, Science Portfolio / Operations, Portefeuil des sciences
 SSC-NRC / SPC-CNRC
 Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
 Halifax, NS  B3H 3Z1
 902 426-1677
 sheldon.bri...@ssc-spc.gc.ca
  
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] tophat2 install

You should be able to click on the missing tool dependency and see its 
installation log.  It should show you whatever error is occuring that is not 
allowing successful installation.

Greg Von Kuster

On Mar 20, 2014, at 9:46 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
wrote:

 Hi,
  
 The repair operation doesn’t seem to make any difference (I already tried 
 that before emailing).  Screenshot of the result attached.
  
 -Sheldon
  
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 10:26 AM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 Hi Sheldon,
  
 I recommend not manually changing any database entries.  You should be able 
 to install the repository and all of its dependencies using the Repair 
 Repository feature.  See 
 https://wiki.galaxyproject.org/RepairingInstalledRepositories
  
 Greg Von Kuster
  
 On Mar 20, 2014, at 8:59 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
 wrote:
 
 
 Hi,
  
 Just wondering if I can still use the following to fix up my messed up 
 tophat2 install (the install had hung up on me, for 2 hours, and I tried to 
 remove/repair it via the interface).  I haven’t had problems installing any 
 other tools or packages.  I am using postgres but this advice was given 2 
 years ago to another user and fields may have changed.  Thanks for any help!
 -Sheldon  
  
 1. Manually remove the installed repository subdirectory hierarchy from disk. 
 2. If the repository included any tools, manually remove entries for each of 
 them from the shed_tool-conf.xml file ( or the equivalent file you have 
 configured for handling installed repositories ) 
 3. Manually update the database using the following command (assuming your 
 installed repository is named 'bcftools_view' and it is the only repository 
 you have installed with that name) - letter capitalization is required: 
 
 The following assumes you're using postgres: 
 
 update tool_shed_repository set deleted=True, uninstalled=True, 
 status='Uninstalled', error_message=Null  where name = 'bcftools_view';
  
  
  
 From: Briand, Sheldon 
 Sent: Wednesday, March 12, 2014 11:44 AM
 To: galaxy-dev@lists.bx.psu.edu
 Subject: tophat2 install
  
 Hi,
  
 I ran into a problem installing tophat2 here:
 tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType 
 found
  
 I have only used the interface to do the installation (no manual deletes).  
 The rest of the dependencies for tophat2 installed just fine.
  
 Repairing the repository doesn’t make any difference.
  
 Thanks!
 -Sheldon
  
 Sheldon Briand
 NRC Research Computing Support Analyst
 Research Computing Support / Soutien Informartique a la Recherche
 Operations, Science Portfolio / Operations, Portefeuil des sciences
 SSC-NRC / SPC-CNRC
 Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
 Halifax, NS  B3H 3Z1
 902 426-1677
 sheldon.bri...@ssc-spc.gc.ca
  
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
  
 Screenshot.png

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] tophat2 install

It looks like your database and file system are out of sync.  Your database 
seems to think you have an installed repository but your file system does not 
seem to have the repository's installation directory.  Can you confirm that 
this is the case?


On Mar 20, 2014, at 11:53 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
wrote:

 Hi,
  
 Here is the error from the paster.log:
  
 Traceback (most recent call last):
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py, line 
 496, in handle_tool_dependencies
 from_install_manager=from_install_manager )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 318, in install_package
 from_install_manager=from_install_manager )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 245, in handle_complex_repository_d
 ependency_for_package
 tool_dependencies_config = get_absolute_path_to_file_in_repository( 
 repo_files_dir, 'tool_dependencies.xml' )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 126, in get_absolute_path_to_file_i
 n_repository
 for root, dirs, files in os.walk( repo_files_dir ):
   File /opt/local/python-2.7.5/lib/python2.7/os.py, line 276, in walk
 names = listdir(top)
 TypeError: coercing to Unicode: need string or buffer, NoneType found
  
 -Sheldon
  
 From: galaxy-dev-boun...@lists.bx.psu.edu 
 [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
 Sent: Thursday, March 20, 2014 10:52 AM
 To: 'Greg Von Kuster'
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 Hi,
  
 Yes the error is:
 Error installing tool dependency package tophat2 version 2.0.9: coercing to 
 Unicode: need string or buffer, NoneType found
  
 -Sheldon
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 10:49 AM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 You should be able to click on the missing tool dependency and see its 
 installation log.  It should show you whatever error is occuring that is not 
 allowing successful installation.
  
 Greg Von Kuster
  
 On Mar 20, 2014, at 9:46 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
 wrote:
  
 
 Hi,
  
 The repair operation doesn’t seem to make any difference (I already tried 
 that before emailing).  Screenshot of the result attached.
  
 -Sheldon
  
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 10:26 AM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 Hi Sheldon,
  
 I recommend not manually changing any database entries.  You should be able 
 to install the repository and all of its dependencies using the Repair 
 Repository feature.  See 
 https://wiki.galaxyproject.org/RepairingInstalledRepositories
  
 Greg Von Kuster
  
 On Mar 20, 2014, at 8:59 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
 wrote:
 
 
 
 Hi,
  
 Just wondering if I can still use the following to fix up my messed up 
 tophat2 install (the install had hung up on me, for 2 hours, and I tried to 
 remove/repair it via the interface).  I haven’t had problems installing any 
 other tools or packages.  I am using postgres but this advice was given 2 
 years ago to another user and fields may have changed.  Thanks for any help!
 -Sheldon  
  
 1. Manually remove the installed repository subdirectory hierarchy from disk. 
 2. If the repository included any tools, manually remove entries for each of 
 them from the shed_tool-conf.xml file ( or the equivalent file you have 
 configured for handling installed repositories ) 
 3. Manually update the database using the following command (assuming your 
 installed repository is named 'bcftools_view' and it is the only repository 
 you have installed with that name) - letter capitalization is required: 
 
 The following assumes you're using postgres: 
 
 update tool_shed_repository set deleted=True, uninstalled=True, 
 status='Uninstalled', error_message=Null  where name = 'bcftools_view';
  
  
  
 From: Briand, Sheldon 
 Sent: Wednesday, March 12, 2014 11:44 AM
 To: galaxy-dev@lists.bx.psu.edu
 Subject: tophat2 install
  
 Hi,
  
 I ran into a problem installing tophat2 here:
 tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType 
 found
  
 I have only used the interface to do the installation (no manual deletes).  
 The rest of the dependencies for tophat2 installed just fine.
  
 Repairing the repository doesn’t make any difference.
  
 Thanks!
 -Sheldon
  
 Sheldon Briand
 NRC Research Computing Support Analyst
 Research Computing Support / Soutien Informartique a la Recherche
 Operations, Science Portfolio / Operations, Portefeuil des sciences
 SSC-NRC / SPC-CNRC
 Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Re: [galaxy-dev] tophat2 install

What version of Galaxy are you running?  You want to look in the tophat2 
repository directory, not its package dependency.  There should be a 
tool_dependencies.xml file in the tophat2's installation directory hierarchy 
somewhere.

On Mar 20, 2014, at 1:12 PM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
wrote:

 Hi,
  
 dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
 contains only:
 env.sh
  
 If that isn’t the right place to look let me know.
  
 -Sheldon
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 2:04 PM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 It looks like your database and file system are out of sync.  Your database 
 seems to think you have an installed repository but your file system does not 
 seem to have the repository's installation directory.  Can you confirm that 
 this is the case?
  
  
 On Mar 20, 2014, at 11:53 AM, Briand, Sheldon 
 sheldon.bri...@ssc-spc.gc.ca wrote:
 
 
 Hi,
  
 Here is the error from the paster.log:
  
 Traceback (most recent call last):
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py, line 
 496, in handle_tool_dependencies
 from_install_manager=from_install_manager )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 318, in install_package
 from_install_manager=from_install_manager )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 245, in handle_complex_repository_d
 ependency_for_package
 tool_dependencies_config = get_absolute_path_to_file_in_repository( 
 repo_files_dir, 'tool_dependencies.xml' )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 126, in get_absolute_path_to_file_i
 n_repository
 for root, dirs, files in os.walk( repo_files_dir ):
   File /opt/local/python-2.7.5/lib/python2.7/os.py, line 276, in walk
 names = listdir(top)
 TypeError: coercing to Unicode: need string or buffer, NoneType found
  
 -Sheldon
  
 From: galaxy-dev-boun...@lists.bx.psu.edu 
 [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
 Sent: Thursday, March 20, 2014 10:52 AM
 To: 'Greg Von Kuster'
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 Hi,
  
 Yes the error is:
 Error installing tool dependency package tophat2 version 2.0.9: coercing to 
 Unicode: need string or buffer, NoneType found
  
 -Sheldon
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 10:49 AM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 You should be able to click on the missing tool dependency and see its 
 installation log.  It should show you whatever error is occuring that is not 
 allowing successful installation.
  
 Greg Von Kuster
  
 On Mar 20, 2014, at 9:46 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
 wrote:
  
 
 Hi,
  
 The repair operation doesn’t seem to make any difference (I already tried 
 that before emailing).  Screenshot of the result attached.
  
 -Sheldon
  
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 10:26 AM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 Hi Sheldon,
  
 I recommend not manually changing any database entries.  You should be able 
 to install the repository and all of its dependencies using the Repair 
 Repository feature.  See 
 https://wiki.galaxyproject.org/RepairingInstalledRepositories
  
 Greg Von Kuster
  
 On Mar 20, 2014, at 8:59 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
 wrote:
 
 
 
 
 Hi,
  
 Just wondering if I can still use the following to fix up my messed up 
 tophat2 install (the install had hung up on me, for 2 hours, and I tried to 
 remove/repair it via the interface).  I haven’t had problems installing any 
 other tools or packages.  I am using postgres but this advice was given 2 
 years ago to another user and fields may have changed.  Thanks for any help!
 -Sheldon  
  
 1. Manually remove the installed repository subdirectory hierarchy from disk. 
 2. If the repository included any tools, manually remove entries for each of 
 them from the shed_tool-conf.xml file ( or the equivalent file you have 
 configured for handling installed repositories ) 
 3. Manually update the database using the following command (assuming your 
 installed repository is named 'bcftools_view' and it is the only repository 
 you have installed with that name) - letter capitalization is required: 
 
 The following assumes you're using postgres: 
 
 update tool_shed_repository set deleted=True, uninstalled=True, 
 status='Uninstalled', error_message=Null  where name = 'bcftools_view';
  
  
  
 From: Briand, Sheldon 
 Sent: Wednesday, March 12, 2014 11:44 AM

Re: [galaxy-dev] tophat2 install

There have been several fixes released to the stable branch that you do not 
have in 12441.  I would recommend doing the following:

hg pull
hg update stable

Then uninstall the tophat2 repository and reinstall it.  See if that makes a 
difference.


On Mar 20, 2014, at 1:30 PM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
wrote:

 $ hg summary
 parent: 12441:dc067a95261d
  
 From the tool_dependencies.xml:
  
 package name=tophat2 version=2.0.9
   repository changeset_revision=8549fd545473 
 name=package_tophat2_2_0_9 owner=devteam 
 prior_installation_required=False toolshed
 =http://toolshed.g2.bx.psu.edu; /
  
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 2:23 PM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 What version of Galaxy are you running?  You want to look in the tophat2 
 repository directory, not its package dependency.  There should be a 
 tool_dependencies.xml file in the tophat2's installation directory hierarchy 
 somewhere.
  
 On Mar 20, 2014, at 1:12 PM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
 wrote:
 
 
 Hi,
  
 dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
 contains only:
 env.sh
  
 If that isn’t the right place to look let me know.
  
 -Sheldon
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 2:04 PM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 It looks like your database and file system are out of sync.  Your database 
 seems to think you have an installed repository but your file system does not 
 seem to have the repository's installation directory.  Can you confirm that 
 this is the case?
  
  
 On Mar 20, 2014, at 11:53 AM, Briand, Sheldon 
 sheldon.bri...@ssc-spc.gc.ca wrote:
 
 
 
 Hi,
  
 Here is the error from the paster.log:
  
 Traceback (most recent call last):
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py, line 
 496, in handle_tool_dependencies
 from_install_manager=from_install_manager )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 318, in install_package
 from_install_manager=from_install_manager )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 245, in handle_complex_repository_d
 ependency_for_package
 tool_dependencies_config = get_absolute_path_to_file_in_repository( 
 repo_files_dir, 'tool_dependencies.xml' )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 126, in get_absolute_path_to_file_i
 n_repository
 for root, dirs, files in os.walk( repo_files_dir ):
   File /opt/local/python-2.7.5/lib/python2.7/os.py, line 276, in walk
 names = listdir(top)
 TypeError: coercing to Unicode: need string or buffer, NoneType found
  
 -Sheldon
  
 From: galaxy-dev-boun...@lists.bx.psu.edu 
 [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
 Sent: Thursday, March 20, 2014 10:52 AM
 To: 'Greg Von Kuster'
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 Hi,
  
 Yes the error is:
 Error installing tool dependency package tophat2 version 2.0.9: coercing to 
 Unicode: need string or buffer, NoneType found
  
 -Sheldon
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 10:49 AM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 You should be able to click on the missing tool dependency and see its 
 installation log.  It should show you whatever error is occuring that is not 
 allowing successful installation.
  
 Greg Von Kuster
  
 On Mar 20, 2014, at 9:46 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
 wrote:
  
 
 Hi,
  
 The repair operation doesn’t seem to make any difference (I already tried 
 that before emailing).  Screenshot of the result attached.
  
 -Sheldon
  
  
 From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
 Sent: Thursday, March 20, 2014 10:26 AM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
  
 Hi Sheldon,
  
 I recommend not manually changing any database entries.  You should be able 
 to install the repository and all of its dependencies using the Repair 
 Repository feature.  See 
 https://wiki.galaxyproject.org/RepairingInstalledRepositories
  
 Greg Von Kuster
  
 On Mar 20, 2014, at 8:59 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca 
 wrote:
 
 
 
 
 
 Hi,
  
 Just wondering if I can still use the following to fix up my messed up 
 tophat2 install (the install had hung up on me, for 2 hours, and I tried to 
 remove/repair it via the interface).  I haven’t had problems installing any 
 other tools or packages.  I am using postgres but this advice was given 2 
 years ago to another user and fields may

Re: [galaxy-dev] tophat2 install

Sorry, should have advised this:

 hg pull https://bitbucket.org/galaxy/galaxy-central#stable
 hg update stable

See the end ot this thread:

http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-td4663719.html




On Mar 20, 2014, at 1:51 PM, Björn Grüning bjoern.gruen...@gmail.com wrote:

 Hi,
 
 you need to track galaxy-central to make use of the patches that are applied 
 as bugfixes after the release. You can do that easily with changing the path 
 in .hg/hgrc ... but I do not know if that is the right way to do ;) For me it 
 worked.
 
 Cheers,
 Bjoern
 
 Am 20.03.2014 18:46, schrieb Briand, Sheldon:
 pulling from https://bitbucket.org/galaxy/galaxy-dist
 searching for changes
 no changes found
 
 From: Greg Von Kuster [mailto:g...@bx.psu.edu]
 Sent: Thursday, March 20, 2014 2:36 PM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
 
 There have been several fixes released to the stable branch that you do not 
 have in 12441.  I would recommend doing the following:
 
 hg pull
 hg update stable
 
 Then uninstall the tophat2 repository and reinstall it.  See if that makes a 
 difference.
 
 
 On Mar 20, 2014, at 1:30 PM, Briand, Sheldon 
 sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote:
 
 
 $ hg summary
 parent: 12441:dc067a95261d
 
 From the tool_dependencies.xml:
 
 package name=tophat2 version=2.0.9
   repository changeset_revision=8549fd545473 
 name=package_tophat2_2_0_9 owner=devteam 
 prior_installation_required=False toolshed
 =http://toolshed.g2.bx.psu.edu; /
 
 
 From: Greg Von Kuster [mailto:g...@bx.psu.eduhttp://bx.psu.edu]
 Sent: Thursday, March 20, 2014 2:23 PM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
 
 What version of Galaxy are you running?  You want to look in the tophat2 
 repository directory, not its package dependency.  There should be a 
 tool_dependencies.xml file in the tophat2's installation directory hierarchy 
 somewhere.
 
 On Mar 20, 2014, at 1:12 PM, Briand, Sheldon 
 sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote:
 
 
 
 Hi,
 
 dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
 contains only:
 env.sh
 
 If that isn't the right place to look let me know.
 
 -Sheldon
 
 From: Greg Von Kuster [mailto:g...@bx.psu.eduhttp://bx.psu.edu]
 Sent: Thursday, March 20, 2014 2:04 PM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
 
 It looks like your database and file system are out of sync.  Your database 
 seems to think you have an installed repository but your file system does 
 not seem to have the repository's installation directory.  Can you confirm 
 that this is the case?
 
 
 On Mar 20, 2014, at 11:53 AM, Briand, Sheldon 
 sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote:
 
 
 
 
 Hi,
 
 Here is the error from the paster.log:
 
 Traceback (most recent call last):
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py, 
 line 496, in handle_tool_dependencies
 from_install_manager=from_install_manager )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 318, in install_package
 from_install_manager=from_install_manager )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 245, in handle_complex_repository_d
 ependency_for_package
 tool_dependencies_config = get_absolute_path_to_file_in_repository( 
 repo_files_dir, 'tool_dependencies.xml' )
   File 
 /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
  line 126, in get_absolute_path_to_file_i
 n_repository
 for root, dirs, files in os.walk( repo_files_dir ):
   File /opt/local/python-2.7.5/lib/python2.7/os.py, line 276, in walk
 names = listdir(top)
 TypeError: coercing to Unicode: need string or buffer, NoneType found
 
 -Sheldon
 
 From: 
 galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu
  
 [mailto:galaxy-dev-boun...@lists.bx.psu.edumailto:dev-boun...@lists.bx.psu.edu]
  On Behalf Of Briand, Sheldon
 Sent: Thursday, March 20, 2014 10:52 AM
 To: 'Greg Von Kuster'
 Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
 
 Hi,
 
 Yes the error is:
 Error installing tool dependency package tophat2 version 2.0.9: coercing to 
 Unicode: need string or buffer, NoneType found
 
 -Sheldon
 
 From: Greg Von Kuster [mailto:g...@bx.psu.edu]
 Sent: Thursday, March 20, 2014 10:49 AM
 To: Briand, Sheldon
 Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu'
 Subject: Re: [galaxy-dev] tophat2 install
 
 You should be able to click on the missing tool dependency and see its

Re: [galaxy-dev] Installing homer into galaxy

Hi Pete,

Here is the recipe for installing homer from this repository:
http://toolshed.g2.bx.psu.edu/view/kevyin/homer  

?xml version=1.0?
tool_dependency
  package name=homer version=4.1
install version=4.1
  actions
action 
type=download_by_urlhttp://biowhat.ucsd.edu/homer/configureHomer.pl/action
action type=shell_commandperl ./configureHomer.pl -install/action
!--action type=shell_commandperl ./configureHomer.pl -install 
hg19/action--
action type=move_directory_files
  source_directory.//source_directory
  destination_directory$INSTALL_DIR/destination_directory
/action
action type=set_environment
  environment_variable name=PATH 
action=prepend_to$INSTALL_DIR/bin/environment_variable
/action
  /actions
/install
readme
  I'm sorry but this does not work
  
/readme
  /package
/tool_dependency

The problem is tha the following tag:

install version=4.1

must be:
install version=1.0

I'm pretty sure a message was displayed when the file was uploaded, but it's 
been a while since I looked at thie relevant code, so I'm not positive.

Gfreg Von Kuster

On Mar 20, 2014, at 2:52 PM, Pete Schmitt peter.r.schm...@dartmouth.edu wrote:

 I've installed homer 4.5 on the server that hosts the latest galaxy version, 
 and ensured that
 it is in galaxy's path (in run.sh) when it starts up.  When installing the 
 wrapper from the main toolshed
 I get the following error which I don't understand:
 
 Tool shed repository: homer
 Tool shed repository changeset revision: f0b5827b6051
 Tool dependency status: Error
 Tool dependency installation error: Error installing tool dependency package 
 homer version 4.1: Only install version 1.0 is currently supported (i.e., 
 change your tag to be ).
 Tool dependency installation directory: 
 /galaxy/tools/homer/4.1/kevyin/homer/f0b5827b6051
 
 The following is the README from the homer wrapper that I installed:
 
 Homer wrapper for Galaxy
 
 The homer tools will need to be accessible from command line
 
 Code repo: https://bitbucket.org/gvl/homer
 
 =:
 LICENSE for this wrapper: 
 =:
 Kevin Ying
 Garvan Institute: http://www.garvan.org.au
 GVL: https://genome.edu.au/wiki/GVL
 
 http://opensource.org/licenses/mit-license.php
 
 
 ___
 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/
 
 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Installing homer into galaxy