galaxy-dev October 2015

galaxy-dev@lists.galaxyproject.org

62 participants
73 discussions

Re: [galaxy-dev] pbs_python can't be installed via scramble
by Makis Ladoukakis 14 Oct '15

14 Oct '15

Hello Will, The second command returns the container.hpp inside the directory of the torque source which i used to install it: find / -name container.hpp /home/user/torque-5.1.1.2-1_18e4a5f1/src/include/container.hpp I noticed there is also a log.h file there. the first command doesn't return anything (I've search manually too, nothing inside /usr/local/include/). How do I fix this? Shall I change the export command of PBS_PYTHON_INCLUDEDIR? Thank you, Makis Date: Thu, 24 Sep 2015 08:31:07 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz(a)lygos.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.galaxyproject.org And does find /usr/local/include -name container.hppor find / -name container.hppreturn torque/src/include/container.hpp ? My guess is you installed binaries for Torque, but the scrambling requires the Torque source (or at least the header files form Torque). -Will On Thu, Sep 24, 2015 at 1:16 AM, Makis Ladoukakis <makis4ever(a)hotmail.com> wrote: Hello Will, Thanks again for your reply. Yes I had already tried these but I got the same container.hpp error. The only thing different in my case is that the names of the directories of the directories are a bit different: export PBS_PYTHON_INCLUDEDIR=/usr/local/include/ export PBSCONFIG=/usr/local/bin/pbs-config export LIBTORQUE_DIR=/usr/local/lib/libtorque.so python scripts/scramble.py -e pbs_python Any ideas? Kind regards, Makis Date: Wed, 23 Sep 2015 07:06:32 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz(a)lygos.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.galaxyproject.org Hi Makis, The thread I posted does have the exact same container.hpp error and proposes a solution. Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include directory, as mentioned in that thread? from the thread:export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/ export PBSCONFIG=/usr/local/torque/bin/pbs-config export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so -Will On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4ever(a)hotmail.com> wrote: Hello Will, Thank you for your reply. I had already checked this thread before as I browsed through the mailing list for "pbs_python" issues. It doesn't have the same errors (can't locate log.h and when i provide it it wants the container.hpp ) and up to one point i've already followed the "rescrambling" of the pbs_python. Anyone else had any experience with that? Thank you, Makis Date: Tue, 22 Sep 2015 09:35:11 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz(a)lygos.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.galaxyproject.org Here is an old thread that looks rather similar to your problems:https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/ms… -Will On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever(a)hotmail.com> wrote: Hello everyone, I'm trying to set up a Galaxy instance on a multi-core server in my university so according to the instructions here: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python and tried to setup pbs_python via scramble: LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python When I did that I got the error: Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0 so I did some digging around and found that the file I need is in /scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ (please correct me if I am wrong) So I tried again using: PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python but then I got the error: In file included from src/C++/pbs_ifl.h:90:0, from src/C++/pbs_wrap.cxx:2978: /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or directory #include "container.hpp" Can someone help me please? Kind regards, Makis ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz(a)lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz(a)lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz(a)lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.

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MS Active Directory Authentication
by McCully, Dwayne (NIH/NIAMS) [C] 13 Oct '15

13 Oct '15

Hello Everyone, Is there an example of the auth_config.xml for a MS Active directory connection? I would like to all my users to register and login to Galaxy with their AD username and password. Note: We don't use a "@example.com" extension for our usernames just "username". Thanks in advance Dwayne

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External User Authenticaion
by Ryan G 13 Oct '15

13 Oct '15

Hi all - I'm trying to use external user authentication with Galaxy. The external authentication passes to Galaxy the username with the mail domain at HTTP_USER. In galaxy.ini, I enable: use_remote_user = True When I try to access Galaxy, I get the message: Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. But nothing in paster.log indicating what the error is. How do I track this down?

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Installing Cairo into Gakaxy
by Christian Brenninkmeijer 13 Oct '15

13 Oct '15

Hi All, Has anyone got a working example tool_dependencies.xml to install the Cairo package into R. (I actually need a package that depends on R Cairo but the current issue is Cairo) I am having the cairo.h not found issue I have cloned https://toolshed.g2.bx.psu.edu/view/devteam/package_cairo_1_12_14/b39299b4b… (and its dependencies) As well as https://toolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/9f2fddb9d6e2 I am trying to use <action type="setup_r_environment"> But can not get the package_cairo to be seen by the R I have tried <action type="set_environment_for_install"> both inside and outside of the setup_r_environment but it does not appear to be working, Full attempted tool_dependencies.xml attached, Thanks in advance Christian University of Manchester

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updated eggs needed for OS X El Capitan compatibility
by Wolfgang Maier 12 Oct '15

12 Oct '15

Hi, today, there was a complaint on the Galaxy Biostar forum that Galaxy fails to start under the new OS X El Capitan (https://biostar.usegalaxy.org/p/14492/). I had noticed this last week already, and that post prompted me to investigate the problem in more detail. The result (now checked on our own Galaxy instance) is that compatibility with El Capitan requires updates to two eggs - amqp and kombu - in the sense that, at least, you can start Galaxy after fixing these two. I haven't checked to see if there are additional run time problems. Hope that information helps, Wolfgang

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GCC2016 Training Day Topic Nominations are now open
by Dave Clements 12 Oct '15

12 Oct '15

Hello all, The 2016 Galaxy Community Conference (GCC2016) <https://wiki.galaxyproject.org/Events/GCC2016> features two full days of training on June 26-27. Each day will have multiple tracks, with each track featuring several sessions throughout the day. GCC2016 will be held at Indiana University <http://indiana.edu/> in Bloomington, Indiana, United States. *GCC2016 Training topics <https://wiki.galaxyproject.org/Events/GCC2016/Training> are nominated by you <http://bit.ly/gcc2016tdnom>, the Galaxy Community.* Please give some thought to what topics you would like to see offered, or that you would like to offer, and then submit them as topic nominations <http://bit.ly/gcc2016tdnom>. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see - Topics nominated for GCC2015 <http://bit.ly/gcc2015vote> - Topics nominated for GCC2014 <http://bit.ly/1s6NtMN> - Topics nominated for GCC2013 <http://bit.ly/1i2j1gN> - The Galaxy Events page <https://wiki.galaxyproject.org/Events>, which lists what training the community is offering outside of GCCs. - Topics that have already been nominated for GCC2016 <https://wiki.galaxyproject.org/Events/GCC2016/Training#Nominated_Topics> *Please nominate a topic now! <http://bit.ly/gcc2016tdnom> * Nominated topics will be published as they come in <https://wiki.galaxyproject.org/Events/GCC2016/Training#Nominated_Topics>. *Topic nomination closes Friday, October, 16.*. Topics will be compiled into a uniform list by the GCC2016 Organizing Committee, and topics will be voted on by the Galaxy Community from October 26 through November 6. Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. Looking forward to a stellar set of nominations, and hoping to see you in Bloomington, GCC2016 Exec Committee <https://wiki.galaxyproject.org/Events/GCC2016/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Get the working directory within the ncbi_blastp_wrapper.xml file
by Ryan Johnson 12 Oct '15

12 Oct '15

Hello all, We are setting up a galaxy instance that will submit jobs to our cluster. We could not get pbs_python to work so we have added all PBS logic to the cheetah template wrapper ncbi_blastp_wrapper.xml. Currently, all jobs are running out of the home directory. We want to add logic to the wrapper which will get the working directory from the JobWrapper class and then change to that directory and run from there. Can anyone help us to access the JobWrapper.working_underscore value? Or suggest a better way to do this? Thank you very much, Ryan -- Ryan S. Johnson, PhD Applications Scientist Center for Advanced Research Computing P: (650) 430-6194 E: rjohns03(a)carc.unm.edu

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Workflow 'Input Dataset' Ressolution Issue
by Marco Albuquerque 12 Oct '15

12 Oct '15

Hello Galaxy Dev, Consider the workflow found in 'Strelka_Workflow_Sequential' image Here it is in a different view 'Strelka_Sequential_Workflow_Different_View' Notice That the first input dataset links to the fetch_interval tool and the first preprocess tool. And the second input dataset links only to the second preprocess tool. When you run the workflow, what actually happens is the first input dataset goes to the fetch_interval tools and the second input dataset goes to both preprocessing tools. (Look at final two images). They have essentially executed the same tool twice. Where it should be an execution with a normal file and an execution with a tumour file. Why is this happening? What can I do to fix this? Thanks, Marco Albuquerque

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Question about using dynamic options and refresh_on_change for rendering 2 associated select lists
by Greg Von Kuster 09 Oct '15

09 Oct '15

Hello all, I’m working on adding support to the Galaxy framework for datatypes in the constructive solid geometry (CSG) space and I have several working Galaxy tools and a visualization plugin that deal with 3d shapes in this environment. All of this work will soon be contributed to open source. For one of the tools, I need to provide 2 select lists on the tool form that are associated in such a way that when an option in select list 1 is chosen, the options in select list 2 are altered and re-rendered. This behavior would probably use a combination of dynamic options and refresh_on_change between the 2 associated select lists. I’ve not seen a tool that does this precisely, so I’m hoping that if it is currently possible to do this within Galaxy tools, someone will point me to an example. If it is not currently possible, I will contribute a PR for supporting it, but would like some input as to how it should be done. Dynamic options are currently rendered using 4 approaches; from_file, from_dataset, from_parameter and from_data_table. One or more of several filters can then be applied to the options to alter them if desired. Since these CSG tools involve new datatypes, I have flexibility into how the metadata elements are set up that are needed to render these 2 select lists. A dictionary may work where the metadata element contents look like this: {a: [‘1’, ‘2’], b: [‘3’, ‘4’] } The options in select list 1 would be ‘a’ and ‘b’. When ‘a’ is selected, select list 2 would have options ‘1’ and ‘2’, and when ‘b’ is selected, select list 2 would have options ‘3’ and ‘4’. To support this approach, perhaps dynamic options could be enhanced to include a from_dict option. There would be some complxity involved in associating the lists using refresh_on_change so that select list 2 is refreshed with the correct options when select list one is changed. I haven’t yet worked out these details. Also, using a dictionary will not keep order for the options, so perhaps a list of tuples would be better? [ [ ‘a’, [‘1’, ‘2’]], [‘b’, [‘3’, ‘4’]]] Can someone let me know if this is currently possible, and if so, an example tool that does it? If it’s not possible, does the above approach seem reasonable, or is there a better way? 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: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>

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Re: [galaxy-dev] Puzzling error in program using Bioblend
by mark fernandes (IFR) 09 Oct '15

09 Oct '15

And it’s Nicola for the win…! I deleted the two tabular files and re-uploaded them and my code works! ☺ Following on from this does this error state happen very often or have I just been unlucky? If the former is true, any suggestions on how best to trap it and report back to user to fix? Thanks Nicola. I was beginning to wonder if I had blundered in my Python. Mark Fernandes T: +44 (0)1603 255000 Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK www.ifr.ac.uk Facebook | Twitter | LinkedIn | YouTube The Institute of Food Research receives strategic funding from BBSRC

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galaxy-dev October 2015