[galaxy-dev] storing set max value in trackster for wig file display
Hi We have been using trackster much more in recent times - It really has improved a lot (especially its stability) over the last few years - thank you very much. We are running into a little annoying issue: when we display wiggle files, bedgraph files, bam files in coverage mode, etc, the max value gets somehow calculated. Very often, we want to change that, ie in order to see the full heights of the peaks instead of the capped peaks. This can be easily done by changing the set max value at the right hand side of the track. Unfortunately, the new value does not get stored. No matter, whether we click on safe or not. So next time we wanna a look at the same visualization again, we have to set the 'max value' again. Is this a known missing feature (bug) ? I just wanna check before I create a Trello card - so far, I couldn't find in in Trello. Thanks for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ 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/
[galaxy-dev] wrong validation message in toolshed
Hi , I'm getting this error message, which is not correct since the file IS available in the repository. Metadata may have been defined for some items in revision 'f70b775dcaa5'. Correct the following problems if necessary and reset metadata. create_model.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. library_lookup.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. query_metexp.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. query_mass_repos.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. rankfilterGCMS_tabular.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. I installed the package anyway and it works, which proves there is no real problem. See https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics2 Regards, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/ ___ 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/
Re: [galaxy-dev] wrong validation message in toolshed
Hi Pieter, there seems to be either multiple incorrect links to the file or the wrappers expect multiple files that are missing from the repo. E.g. your wrapper library_lookup.xml refers to a file /GCMS/match_library.py which does not exist. (on this line: code file=match_library.py /) After you correct these links you might want to 'Reset repository metadata'. Martin On Thu, Mar 19, 2015 at 8:18 AM Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi , I’m getting this error message, which is not correct since the file IS available in the repository. Metadata may have been defined for some items in revision 'f70b775dcaa5'. Correct the following problems if necessary and reset metadata. *create_model.xml* - This file refers to a missing file *match_library.py*. Upload a file named *match_library.py* to the repository to correct this error. *library_lookup.xml* - This file refers to a missing file *match_library.py*. Upload a file named *match_library.py* to the repository to correct this error. *query_metexp.xml* - This file refers to a missing file *match_library.py*. Upload a file named *match_library.py* to the repository to correct this error. *query_mass_repos.xml* - This file refers to a missing file *match_library.py*. Upload a file named *match_library.py* to the repository to correct this error. *metams_lcms_annotate.xml* - This file refers to a missing file *match_library.py*. Upload a file named *match_library.py* to the repository to correct this error. *rankfilterGCMS_tabular.xml* - This file refers to a missing file *match_library.py*. Upload a file named *match_library.py* to the repository to correct this error. *metams_lcms_annotate.xml* - This file refers to a missing file *match_library.py*. Upload a file named *match_library.py* to the repository to correct this error. I installed the package anyway and it works, which proves there is no real problem. See https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics2 Regards, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl ___ 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/ ___ 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/
[galaxy-dev] Problems installing package_bx_python_0_7 from Tool Shed
Hello all, I'm trying to install the intersect tool from the main Tool Shed, https://toolshed.g2.bx.psu.edu/view/devteam/intersect One of the dependencies fails to install, with the cryptic message Initializing repository installation failed [OK]: https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7 Un-installing and reinstalling also fails. $ hg log | head changeset: 14342:db520d154716 branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Thu Sep 04 10:00:23 2014 -0400 summary: Update tag latest_2014.08.11 for changeset e8453771b1db This looks like the relevant chunk from the pasteur.log file: 143.xx.xx.120 - - [19/Mar/2015:12:21:46 +0100] POST /galaxy/admin_toolshed/deactivate_or_uninstall_repository?id=31fe793505d893ac HTTP/1.1 302 - http://ppserver/galaxy/admin_ toolshed/deactivate_or_uninstall_repository?id=31fe793505d893ac Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:36.0) Gecko/20100101 Firefox/36.0 /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/ven + Usage of try_run is deprecated: please do not use it anymore, and avoid configuration checks involving running executable on the target machine. + Traceback (most recent call last): File /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/bin/pip, line 8, in module File /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/__init__.py, line 149, in main File /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/basecommand.py, line 181, in main File /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/log.py, line 48, in fatal File /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/log.py, line 75, in log File /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/backwardcompat/__init__.py, line 88, in fwrite ValueError: I/O operation on closed file 143.xx.xx.120 - - [19/Mar/2015:12:21:47 +0100] GET /galaxy/admin_toolshed/browse_repositories?status=donemessage=The+repository+named+%3Cb%3Epackage_bx_python_0_7%3C%2Fb%3E+has+been+uninstalled.++ HTTP/1.1 200 - http://ppserver/galaxy/admin_toolshed/deactivate_or_uninstall_repository?id=31fe793505d893ac; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:36.0) Gecko/20100101 Firefox/36.0 DeprecationWarning) v/build/numpy/numpy/distutils/command/config.py:40: DeprecationWarning: C compiler: gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python2.6 -c' gcc: _configtest.c gcc -pthread _configtest.o -o _configtest failure. removing: _configtest.c _configtest.o _configtest building data_files sources build_src: building npy-pkg config files Downloading/unpacking bx-python==0.7.1 (from -r /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt (line 3)) Running setup.py egg_info for package bx-python _configtest Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.10.tar.gz Now working in /mnt/galaxy/galaxy-dist/database/tmp/tmpes1qm8/distribute-0.6.10 Extracting in /mnt/galaxy/galaxy-dist/database/tmp/tmpes1qm8 Building a Distribute egg in /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/build/bx-python ute-0.6.10-py2.6.egg Installed /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/build/bx-python/nose-1.3.4-py2.6.egg Installing collected packages: numpy, bx-python Running setup.py install for numpy Error unknown encoding: string-escape while executing command /mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/bin/python -c import
Re: [galaxy-dev] wrong validation message in toolshed
Hi Martin, Thanks. I fixed the problems in the .xml files, now referring to “../match_library.py” . Now the error I get when I try to reset the repository metadata is 502: 502 Bad Gateway nginx/1.2.1 Regards, Pieter From: Martin Čech [mailto:mar...@bx.psu.edu] Sent: donderdag 19 maart 2015 15:02 To: Lukasse, Pieter; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] wrong validation message in toolshed Hi Pieter, there seems to be either multiple incorrect links to the file or the wrappers expect multiple files that are missing from the repo. E.g. your wrapper library_lookup.xml refers to a file /GCMS/match_library.py which does not exist. (on this line: code file=match_library.py /) After you correct these links you might want to 'Reset repository metadata'. Martin On Thu, Mar 19, 2015 at 8:18 AM Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi , I’m getting this error message, which is not correct since the file IS available in the repository. Metadata may have been defined for some items in revision 'f70b775dcaa5'. Correct the following problems if necessary and reset metadata. create_model.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. library_lookup.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. query_metexp.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. query_mass_repos.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. rankfilterGCMS_tabular.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error. I installed the package anyway and it works, which proves there is no real problem. See https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics2 Regards, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/ ___ 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/ ___ 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/
