galaxy-dev September 2013

galaxy-dev@lists.galaxyproject.org

93 participants
174 discussions

Tool Shed packages for BLAST+ binaries
by Peter Cock 03 Sep '13

03 Sep '13

Hi Greg et al, For the NCBI BLAST+ wrappers, Nicola has suggested we split out the binaries themselves into a separate Tool Shed package, e.g. package_blast_plus_2_2_26 and similar for the later releases. https://github.com/peterjc/galaxy_blast/issues/7 I think this is a good idea. I'd like to check if there are any complications foreseeable from the fact that the NCBI BLAST+ wrappers were migrated out of the Galaxy core and therefore have migration scripts we need to consider. Potentially this could be held under the shared IUC account as planned for other commonly used packages? Or would the migration issues require it to also live under devteam? Also, we may wish to add a dependency on BOOST, e.g. http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 once this is on the main Tool Shed. Regards, Peter

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[GSoC2013] Week 9,10,11 Update
by Saket Choudhary 02 Sep '13

02 Sep '13

Update here : http://galaxy-gsoc2013.blogspot.in/2013/09/blog-post.html -- Saket

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Postgresql database cleaning
by Christophe Antoniewski 01 Sep '13

01 Sep '13

Hi everybody, The python scripts to clean histories, datasets, users etc.. are fine... However, the records are not really removed from the postgresql database and as a result, this one gets bigger and bigger with unused records. Ours is above 1 To after 2 years of production. Is there a safe way to clean the database from unused records and their dependencies to reduce it size, without being a postgresql guru ? Chris -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org

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Re: [galaxy-dev] [galaxy-user] About tool classify in the tool box panel
by Björn Grüning 01 Sep '13

01 Sep '13

Hi, try that: <label text="GFF" id="gff" /> Cheers, Bjoern > Dear Bjoern > > > I know that the "name" define sections name, however what I want to > fulfill is to part section into several groups. Just like the > following figure shows. > > > 内嵌图片 1 > > > I want to add the "NGS TOOLBOX BETA" and "REGENETICS"--- this kind of > classify function. > > > Do you know how to fulfill it in my local Galaxy? > > > Thank you for your reply. > > > Regards, > XiaoTao > > > > 2013/8/31 Bjoern Gruening <bjoern.gruening(a)gmail.com> > Hi Xiao, > > have a look in your tool_conf.xml file. > > <section name="Send Data" id="send"> > <tool file="data_destination/epigraph.xml" /> > <tool file="data_destination/epigraph_test.xml" /> > <tool file="genomespace/genomespace_exporter.xml" /> > </section> > > You can specify sections with the section tag. Keep in mind > that the ID > needs to be unique. > > Cheers, > Bjoern > > > Dear all > > > > > > I want to know how to part the tool panel into several group > just like > > the public Galaxy. It classify the tools into NGS Tools Box > and > > RECENTS. I can not find tag that up <section> tag in the > wiki > > document. Anyone can tell me how to configure to classify > tools? > > > > > > Thank you for all your help > > > > > > Regards, > > Xiaotao JIANG > > The University of HongKong > > > ___________________________________________________________ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org. Please keep all replies on the list by > > using "reply all" in your mail client. For discussion of > > local Galaxy instances and the Galaxy source code, please > > use the Galaxy Development list: > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > 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/ > > > > >

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galaxy-dev September 2013