March 2013 - galaxy-dev - lists.galaxyproject.org

Error while installing DESeq-hts
by Philipe Moncuquet 01 Mar '13

01 Mar '13

Hi, I have tried to follow instructions provided with this installation a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts. I successfully ran the setup scrip but is there other path and conf that need to be done apart from those done by this script ? b) Inside the mex folder execute the make file to create platform dependent .mex files cd mex/Makefile make [interpreter] make octave for octave make matlab for matlab make all for octave and matlab When I run make octave I get the following error message : /usr/bin/mkoctfile -g --mex get_reads.cpp get_reads_direct.cpp mex_input.cpp read.cpp -I/mnt/galaxyTools/tools/samtools/0.1.16 -L/mnt/galaxyTools/tools/samtools/0.1.16 -lbam -lz -lcurses get_reads_direct.cpp:14:17: fatal error: sam.h: No such file or directory compilation terminated. make: *** [get_reads.mex] Error 1 It feels like this is link to samtools, when browsing on the web I found information about SAMTOOLS_ROOT env variable but changing this one doesn't solve my problem. As anyone else encounter this kind of things ? Regards, Philippe

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March 2013 Galaxy Update
by Dave Clements 28 Feb '13

28 Feb '13

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Error on the sandbox toolshed when updating files
by Peter Waltman 28 Feb '13

28 Feb '13

Hi - I was only trying to upload a new gzipped-tarfile with new files to a repository that I own on the sandbox toolshed server, and get the following error: Server ErrorURL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d… Module paste.exceptions.errormiddleware:*144* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*128* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*184* in handle_request >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*94* in decorator >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.webapps.tool_shed.controllers.upload:*108* in upload >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> self*.*upload_tar*(* trans*,* repository*,* tar*,* uploaded_file*,* upload_point*,* remove_repo_files_not_in_tar*,* commit_message*,* new_repo_alert *)* Module galaxy.webapps.tool_shed.controllers.upload:*283* in upload_tar >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* self*.*__handle_directory_changes*(*trans*,* repository*,* full_path*,* filenames_in_archive*,* remove_repo_files_not_in_tar*,* new_repo_alert*,* commit_message*,* undesirable_dirs_removed*,* undesirable_files_removed*)* Module galaxy.webapps.tool_shed.controllers.upload:*345* in __handle_directory_changes >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> commands*.*commit*(* repo*.*ui*,* repo*,* full_path*,* user*=*trans*.*user*. *username*,* message*=*commit_message *)* Module mercurial.commands:*1279* in commit >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> node *=* cmdutil*.*commit*(*ui*,* repo*,* commitfunc*,* pats*,* opts*)* Module mercurial.cmdutil:*1294* in commit >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> scmutil*.*match*(*repo*[*None*]**,* pats*,* opts*)**,* opts*)* Module mercurial.commands:*1277* in commitfunc >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> match*,* editor*=*e*,* extra*=*extra*)* Module mercurial.localrepo:*1199* in commit >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> ret *=* self*.*commitctx*(*cctx*,* True*)* Module mercurial.localrepo:*1270* in commitctx >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> p2*.*manifestnode*(**)**,* *(*new*,* drop*)**)* Module mercurial.manifest:*197* in add >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> cachedelta *=* *(*self*.*rev*(*p1*)**,* addlistdelta*(*addlist*,* delta*)**) * Module mercurial.manifest:*124* in addlistdelta >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> addlist*[*start*:*end*]* *=* array*.*array*(*'c'*,* content*)* *TypeError: array item must be char* Is there a better way to upload updated files to those repositories? -- Peter Waltman, Ph.D. pwaltman(a)ucsc.edu 617.347.187

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Coming soon: BOSC/Broad Hackathon, SciPy Bioinformatics, BOSC Codefest
by Brad Chapman 28 Feb '13

28 Feb '13

Hi all; There are some upcoming coding events and conferences of interest to open source biology programmers: - BOSC/Broad Interoperability Hackathon -- This is a two day coding session at the Broad Institute in Cambridge, MA on April 7-8 focused on improving tool interoperability. Sign up and details: http://j.mp/XJT6ew - SciPy 2013 -- The Scientific Python conference is June 26-27 in Austin and has a Bioinformatics mini-symposia this year. They're doing some great work like IPython, NumPy, SciPy and scikit-learn; and this is a nice opportunity to reach a new set of like minded programmers and expand the open source bioinformatics community. Bioinformatics mini-symposia: http://j.mp/Z4xxXB Abstract details: http://conference.scipy.org/scipy2013/about.php - Codefest at the Bioinformatics Open Source Conference -- This year BOSC is taking place in Berlin from July 19-20 and we'll have a two day coding session before the conference. This is the 4th year of Codefests and they've proven to be a productive and fun time to work collectively on open source projects. Sign up and details: http://www.open-bio.org/wiki/Codefest_2013 BOSC conference: http://www.open-bio.org/wiki/BOSC_2013 Here are the key dates for the events and abstracts: March 20, 2013: SciPy abstracts due April 7-8, 2013: BOSC/Broad Interoperability Hackathon, Cambridge, MA April 12, 2013: BOSC abstracts due June 24-29, 2013: SciPy in Austin, TX July 17-18, 2013: Codefest 2013, Berlin July 19-20, 2013: BOSC 2013, Berlin Looking forward to seeing everyone this spring and summer for plenty of fun science and code, Brad

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cleanup script fails on dataset_instance "None"
by Anthonius deBoer 28 Feb '13

28 Feb '13

Hi, I have some problems with the cleanup scripts... I seem to have a dataset_instance that is "None" and if it tries to delete that you obviously get an error. (See below..>I added the print statement, but the line is the same)... I wonder how I could get a dataset with a None definition and how can I clean up the database for this? Thanks, Thon sh < purge_libraries.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 527, in <module> if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 122, in main purge_libraries( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 217, in purge_libraries _purge_folder( library.root_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 500, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 500, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 500, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 498, in _purge_folder _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable File "./scripts/cleanup_datasets/cleanup_datasets.py", line 376, in _purge_dataset_instance print('dataset_instance.id: {0}'.format(dataset_instance.id)) AttributeError: 'NoneType' object has no attribute 'id' (galaxy_env)[svcgalaxy@srv151 cleanup_datasets]$ sh < purge_libraries.sh

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