- galaxy-dev - lists.galaxyproject.org

(no subject)
by Jager, Victor de 04 Apr '16

04 Apr '16

Dear Galaxy Team, I'm trying to install the repeatexplorer tool https://bitbucket.org/repeatexplorer/ I get the following message that I cannot solve. it does not seem to be releated to the repeatexplorer tool itself since it is not using MPI as far as I can tell although it does not seem to happen with other tools at the galaxy instance. ERROR: ld.so: object '/usr/lib/openmpi/lib/libmpi.so' from LD_PRELOAD cannot be preloaded (wrong ELF class: ELFCLASS64): ignored. note: /usr/lib/openmpi/lib/libmpi.so exists and is a 64 bits lib I've tried unsetting the LD_PRELOAD library for the galaxy user but that did not help,. According to the logs it looks like this error occurs after the job finishes. I would appreciate any clues on how to debug this and to find out where this message comes from. below the snippet from the logfiles: galaxy.jobs DEBUG 2016-04-04 11:22:40,544 (1829) Working directory for job is: /mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829 galaxy.jobs.handler DEBUG 2016-04-04 11:22:40,556 (1829) Dispatching to drmaa runner galaxy.jobs DEBUG 2016-04-04 11:22:40,760 (1829) Persisting job destination (destination id: sge_default) galaxy.jobs.runners DEBUG 2016-04-04 11:22:40,765 Job [1829] queued (207.994 ms) galaxy.jobs.handler INFO 2016-04-04 11:22:40,808 (1829) Job dispatched galaxy.jobs.runners DEBUG 2016-04-04 11:22:41,841 (1829) command is: bash /mnt/data/home/NIOO/galaxy/galaxy-dist/tools/umbr_programs/seqclust/seqclust-main.sh -s /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3137.dat -m 0.01 -o 40 -d Viridiplantae -v /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3173.dat -w /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3174.dat -y /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3175.dat -z RMSKtable -r /mnt/data/home/NIOO/galaxy/galaxy-dist -t /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3176.dat -u '/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/dataset_3176_files' -p false -f 0 -a True -l 55 -x " " -K 10; return_code=$?; python "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/set_metadata_VcdaXP.py" "/tmp/tmpOOJhc4" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/galaxy.json" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2937_ivd_QV,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2937__9U8lt,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2937_zmXF2T,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2937_XHZd2p,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3176.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2937_0_rQHI" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2936_2FIF61,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2936__PZplz,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2936_ImcuR2,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2936_Jm3zxC,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3175.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2936_qkgfR7" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2935_5Ozbvu,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2935_H_7TWw,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2935_Rp42fp,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2935_ycng_Q,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3174.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2935_gbk6Im" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2934_wM1GtU,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2934_pUrJqr,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2934__8Jvh6,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2934_n_AZt2,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3173.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2934_ovKSAZ" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:41,890 (1829) submitting file /mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/galaxy_1829.sh galaxy.jobs.runners.drmaa INFO 2016-04-04 11:22:41,900 (1829) queued as 9507 galaxy.jobs DEBUG 2016-04-04 11:22:41,950 (1829) Persisting job destination (destination id: sge_default) galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:42,159 (1829/9507) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:44,286 (1829/9507) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:47:59,005 (1829/9507) state change: job finished normally galaxy.jobs DEBUG 2016-04-04 11:47:59,500 setting dataset state to ERROR galaxy.jobs DEBUG 2016-04-04 11:47:59,527 setting dataset state to ERROR galaxy.jobs DEBUG 2016-04-04 11:47:59,559 setting dataset state to ERROR galaxy.jobs DEBUG 2016-04-04 11:47:59,602 setting dataset state to ERROR galaxy.jobs INFO 2016-04-04 11:47:59,779 Collecting job metrics for <galaxy.model.Job object at 0x7f3f346d89d0> galaxy.jobs DEBUG 2016-04-04 11:47:59,798 job 1829 ended (finish() executed in (595.557 ms))

2 1

MySQL & ToolShed installs: 'latin-1' codec can't encode character
by Peter Cock 04 Apr '16

04 Apr '16

Hello all, We just ran into a Tool Shed installation problem under a test installation of Galaxy v16.01, while trying to install the meme_fimo tool. Clicking through the GUI takes me to the failed install of the perl_xml_parser_expat version 2.41 package (under package_perl_xml_parser_expat_2_41), https://toolshed.g2.bx.psu.edu/view/iuc/package_perl_xml_parser_expat_2_41v… https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_per… The Admin GUI shows this long stack trace error: File "/mnt/qnap/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 123, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "/mnt/qnap/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 81, in install_and_build_package initial_download=True ) File "/mnt/qnap/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/mnt/qnap/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 1253, in execute_step job_name=package_name) File "/mnt/qnap/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 140, in handle_command error_message=error_message) File "/mnt/qnap/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py", line 390, in set_tool_dependency_attributes sa_session.flush() File "/mnt/shared/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 150, in do return getattr(self.registry(), name)(*args, **kwargs) ... File "/mnt/shared/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 187, in execute query = query % tuple([db.literal(item) for item in args]) File "/mnt/shared/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 278, in literal return self.escape(o, self.encoders) File "/mnt/shared/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 208, in unicode_literal return db.literal(u.encode(unicode_literal.charset)) 'latin-1' codec can't encode character u'\u2018' in position 1070: ordinal not in range(256) This is the left single quotation mark (U+2018), which I think comes from the failed installation log: $ tail /mnt/shared/galaxy/tool_dependency_dir/perl_xml_parser_expat/2.41/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9/INSTALLATION.log Expat.xs:2179: error: ‘parser’ undeclared (first use in this function) Expat.xs:2180: error: ‘CallbackVector’ has no member named ‘st_serial’ Expat.xs:2182: error: ‘CallbackVector’ has no member named ‘skip_until’ Expat.c: In function ‘XS_XML__Parser__Expat_Do_External_Parse’: Expat.c:2904: error: ‘XML_Parser’ undeclared (first use in this function) Expat.c:2904: error: expected ‘;’ before ‘parser’ Expat.xs:2194: error: ‘parser’ undeclared (first use in this function) make[1]: *** [Expat.o] Error 1 make: *** [subdirs] Error 2 ############################################# Note those fancy quote characters? Yep: $ hexdump -C /mnt/shared/galaxy/tool_dependency_dir/perl_xml_parser_expat/2.41/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9/INSTALLATION.log | tail -n 15 00022e90 6f 72 3a 20 65 78 70 65 63 74 65 64 20 e2 80 98 |or: expected ...| 00022ea0 3b e2 80 99 20 62 65 66 6f 72 65 20 e2 80 98 70 |;... before ...p| 00022eb0 61 72 73 65 72 e2 80 99 0a 45 78 70 61 74 2e 78 |arser....Expat.x| 00022ec0 73 3a 32 31 39 34 3a 20 65 72 72 6f 72 3a 20 e2 |s:2194: error: .| 00022ed0 80 98 70 61 72 73 65 72 e2 80 99 20 75 6e 64 65 |..parser... unde| 00022ee0 63 6c 61 72 65 64 20 28 66 69 72 73 74 20 75 73 |clared (first us| 00022ef0 65 20 69 6e 20 74 68 69 73 20 66 75 6e 63 74 69 |e in this functi| 00022f00 6f 6e 29 0a 6d 61 6b 65 5b 31 5d 3a 20 2a 2a 2a |on).make[1]: ***| 00022f10 20 5b 45 78 70 61 74 2e 6f 5d 20 45 72 72 6f 72 | [Expat.o] Error| 00022f20 20 31 0a 6d 61 6b 65 3a 20 2a 2a 2a 20 5b 73 75 | 1.make: *** [su| 00022f30 62 64 69 72 73 5d 20 45 72 72 6f 72 20 32 0a 23 |bdirs] Error 2.#| 00022f40 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 |################| * 00022f60 23 23 23 23 23 23 23 23 23 23 23 23 0a |############.| 00022f6d Notice the sequence in hex of e2 80 98, that's the UTF-8 (hex) for the problem character. We also have e2 80 99 which is the matching right single quote. While I can go over the full INSTALLATION.log to work out what might be wrong, there is clearly a Galaxy problem with the UTF-8 encoded character. Going over the Galaxy mailing list there have been similar problems (although not ToolShed related) reported in the past (2013) with MySQL and the table encodings: http://dev.list.galaxyproject.org/error-with-unicode-output-td4662783.html Are there still known issues with encodings and the MySQL galaxy schema? Are we likely to run into other corner cases with MySQL where we would be better off switching to PostgreSQL? Regards, Peter

1 1

init scripts version 16.01
by Eric Kuyt 02 Apr '16

02 Apr '16

Hey guys, today I updated to the latest version of galaxy. No I noticed that because of the new virtualenv/wheel startup procedure, the init scripts as mentioned here https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28… are not working anymore. Whet is the new startup procedure? Thanks Eric Kuijt -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt(a)wur.nl Web: http://www.cvi.wur.nl

2 2

Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from etiennewalex@yahoo.fr (megablast_wrapper)
by Jennifer Hillman-Jackson 01 Apr '16

01 Apr '16

Hi Etienne, Sorry, I didn't notice that the job was run on the test server. The root of the problem could be that the job output exceeds quota. Running the job there will not get around quota, even if the tool has other issues on test that are triggering the failure (is possible - we do test on that server). If the tool did run, and the output hits your account, if it is over quota (10 GB) no more jobs will be permitted to run. It might be best to consider using a local or cloud Galaxy. I do not know when the Fetch Taxonomy tool will be restored to Main (or if yet). Thanks, Jen -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org On Thu, Mar 31, 2016 at 9:08 PM, etienne waleckx <etiennewalex(a)yahoo.fr> wrote: > Gracias Jenifer, > > I re-ran the tool but the same happens. It is strange as when running the > same tool with the same file in usegalaxy it is working well but I can't in > testgalaxy. > I want to run it in testgalaxy so I can use the fetch taxonomic > representation tool after. I already have the Megablast file but I can't > upload it directly to testgalazxy as it semms too big, so I would like to > run the megablast in testgalaxy, then fetch taxonomic representtion. > > Thanks for your help! > > Etienne > > > > > ------------------------------ > *De :* Jennifer Hillman-Jackson <jen(a)galaxyproject.org> > *À :* "galaxy-bugs(a)bx.psu.edu" <galaxy-bugs(a)bx.psu.edu> > *Cc :* etiennewalex(a)yahoo.fr > *Envoyé le :* Jeudi 31 mars 2016 18h03 > *Objet :* Re: [galaxy-bugs] Galaxy tool error report from > etiennewalex(a)yahoo.fr (megablast_wrapper) > > Hello, > > Please re-run the tool as this was most likely a transient cluster failure. > > Our apologies for any confusion, > > Jen > > -- > Jennifer Hillman-Jackson > Galaxy Application Support > http://usegalaxy.org > http://galaxyproject.org > http://biostar.usegalaxy.org > > > On Wed, Mar 30, 2016 at 11:09 PM, <galaxy-bugs(a)bx.psu.edu> wrote: > > > GALAXY TOOL ERROR REPORT > ------------------------ > > This error report was sent from the Galaxy instance hosted on the server > "https://test.galaxyproject.org/" > > ----------------------------------------------------------------------------- > This is in reference to dataset id 763833 (c5a49985053f8bd3) from history > id 328501 (aa1b4cb871c5e196) > > ----------------------------------------------------------------------------- > You should be able to view the history containing the related history item > (83ca2a7d5534e19e) > > 2: Megablast on data 1 > > by logging in as a Galaxy admin user to the Galaxy instance referenced > above > and pointing your browser to the following link. > > https://test.galaxyproject.org/history?id=aa1b4cb871c5e196 > > ----------------------------------------------------------------------------- > The user 'etiennewalex(a)yahoo.fr' provided the following information: > > Hi, > > Can you help me? I don't find why the tool is not running with this > dataset, > > Thanks! > > Etienne > > ----------------------------------------------------------------------------- > info url: > https://test.galaxyproject.org/datasets/83ca2a7d5534e19e/show_params > job id: 529174 (5c8c4452f3c278b5) > tool id: > toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.… > tool version: 1.2.0 > job pid or drm id: 529174 > job tool version: None > > ----------------------------------------------------------------------------- > job command line: > None > > ----------------------------------------------------------------------------- > job stderr: > > > ----------------------------------------------------------------------------- > job stdout: > > > ----------------------------------------------------------------------------- > job info: > Remote job server indicated a problem running or monitoring this job. > > ----------------------------------------------------------------------------- > job traceback: > None > > ----------------------------------------------------------------------------- > (This is an automated message). > > > > >

1 0

About Local Galaxy Tool Problem
by Ferhat Güzel 01 Apr '16

01 Apr '16

Hi, I want to convert .bcl file (data from illumina NextSeq500) to fastq. Firstly, i tried Galaxy on public server and it became success. But i have large dataset and i couldnt wait for weeks to solve. Then, i set up Galaxy locally. But most of tools dissappared in menu. I tried to upload published workflows but i had too many errors. I couldnt do any analysis on local host. What can i do now? Regards, Ferhat GÜZEL

1 0

IUC Hackathon - Conda dependencies
by Rémi MARENCO 01 Apr '16

01 Apr '16

Hi! On monday 04/04, @bgruening <https://github.com/bgruening> and some members of Galaxy team (me and @nitesh1989 <https://github.com/nitesh1989> at least) would want to get a Hackathon on adding IUC / Devteam tools Conda dependencies. Hackathon begins at: 2pm (UTC-4) / 8pm (UTC+2). It will be as following: - @bgruening <https://github.com/bgruening> will give a small introduction how to create a recipe and the scripts involved in it] - Introduce everyone to conda and bioconda - Then we pick a simple tool and create it - @bgruening <https://github.com/bgruening> will provide a list with bugs that needs to be fixed on the framework level Aims: - get familiar with conda packaging the conda-Galaxy integration - remove tools from the testing blacklists: 1 <https://github.com/galaxyproject/tools-iuc/blob/master/.tt_blacklist> 2 <https://github.com/galaxyproject/tools-devteam/blob/master/.tt_blacklist> 3 <https://github.com/bgruening/galaxytools/blob/master/.tt_blacklist> - Integrate Travis-conda testing in GalaxyP - Integrate Travis-conda testing in galaxy_blast (@peterjc <https://github.com/peterjc>?) Infrastructure work: - galaxyproject/galaxy#2047 <https://github.com/galaxyproject/galaxy/issues/2047> - condarc is update if you add new channels, but you can not remove channels - conda is not working in the Galaxy Docker image - bioconda needs to archive all tarballs to depot.galaxyproject.org - Galaxy Admin support to remove environments Let us know <https://github.com/galaxyproject/tools-iuc/issues/700> if you are interested :). Regards, Bjorn, Remi and the Galaxy Team

1 0

Sandbox repository item says "This revision can be installed: False
by rbrown1422＠comcast.net 01 Apr '16

01 Apr '16

Good afternoon, I loaded a tool into the Galaxy https://testtoolshed.g2.bx.psu.edu/ toolshed. It is an xml and python module. It accepted the file fine but with the following output Sharable link to this repository:https://testtoolshed.g2.bx.psu.edu/view/insilico-bob/mean_center… Clone this repository:hg clone https://insilico-bob@testtoolshed.g2.bx.psu.edu/repos/insilico-bob/mean_cen… Repository type:Unrestricted This repository's type cannot be changed because its contents are valid only for its current type or it has been cloned. Revision:4:ac64a6acfdaf This revision can be installed: False Times cloned / installed: 0 =========================== I cannot see the tool when I search on it from my Galaxy instance or from the test shed itself. FYI, I did not add a test scenario to the load. What am I missing? How do I correct this. thanks, Bob

2 1

Problem on postgress database
by jarod_v6＠libero.it 01 Apr '16

01 Apr '16

Hi! I have centos 6.7 and I have install galaxy. I setup galaxy.ini with: database_connection = postgresql://user:password@localhost/galaxydb # TYPE DATABASE USER CIDR-ADDRESS METHOD # "local" is for Unix domain socket connections only local all all trust # IPv4 local connections: host all all 127.0.0.1/32 trust # IPv6 local connections: host all all ::1/128 trust host all all 0.0.0.0/0 trust host all all 127.0.0.1/32 trust host galaxydb galaxy 127.0.0.1/32 md5 and I have the database postgres=# \l List of databases Name | Owner | Encoding | Collation | Ctype | Access privileges -------------+----------+----------+-------------+-------------+----------------------- galaxy_prod | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/postgres : postgres=CTc/postgres : galaxy=CTc/postgres galaxydb | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/postgres : postgres=CTc/postgres : galaxy=CTc/postgres what can I do?

1 0

Galactic News! April Edition: GCC2016, DevOps, Hacks, events, papers, jobs, servers, hub entries, releases, tools
by Dave Clements 31 Mar '16

31 Mar '16

Hello all, The *April Galaxy News <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04>* brings more than the usual amount of *News of the Galaxy*. First, there are a plethora of events coming up around the world: - GCC2016 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#GCC2016>: - *Oral abstracts due April 8 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#GCC2016_Abstract_Deadl…>* - *Scholarship applications due May 1 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Scholarships:_Applicat…>* - Register now and save big <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#GCC2016_Early_Registra…> - Please welcome the the Indiana Health Industry Forum (IHIF) <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Sponsors> as a GCC2016 Sponsor - Two events sponsored by ELIXIR (and others) are coming up, both prominently featuring Galaxy: - Galaxy DevOps Workshop <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Galaxy_DevOps_Workshop…>, 6-7 April, Heidelberg, Germany. *And there is still space.* - Hackathon: Tools, Workflows and Workbenches <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Hackathon:_Tools.2C_Wo…>, 18-20 May, Paris, France - There is also a report from the RADSeq Tools and Workflows Hackathon <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Report:_IUC_Contributi…> held in March. - Plus 12 additional events <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Upcoming_Events> on three continents over the next three months. A lot of *new* - Papers <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#New_Papers> (86 of them, 6 highlighted) - Open positions <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Who.27s_Hiring> (10 of them) - Halogen Bonding <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#New_Public_Galaxy_Serv…> Galaxy server - Galaxy Community Hub <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Galaxy_Community_Hubs> entries (4 of them) - Releases <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Releases> (Planemo <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Planemo_0.24.0> and CloudMan <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#CloudMan_16.03>) - ToolShed Contributions <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#ToolShed_Contributions> And some other news <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Other_News> too. Happy April, Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

Toolshed Question, In reference to https://toolshed.g2.bx.psu.edu/view/youngkim/ezbamqc/caed0168f704
by Molik, David 30 Mar '16

30 Mar '16

We're uploading a tool to the Galaxy Toolshed and were wondering about sample files: Should .loc.sample files refer to sample data ( test-data ) or should they be generalized for integration into other instances of Galaxy? Also, how should dependencies be noted? Best, Dave

2 1