galaxy-dev January 2016

galaxy-dev@lists.galaxyproject.org

59 participants
80 discussions

logged in as 'user2' externally, but has a cookie as 'user1' invalidating session
by Floreline TOUCHARD 05 Jan '16

05 Jan '16

Hi all, happy new year ! I finally manage to connect my Galaxy instance with my NIS service for external authentication but I have a few questions about it : - when I log in with another external account I get the following warning : "galaxy.web.framework.webapp WARNING 2016-01-05 11:52:24,741 User logged in as 'user2(a)example.fr' externally, but has a cookie as 'user1(a)example.fr' invalidating session". I don't know if it's related to the Apache settings or to the browser. Is it a problem or just a warning that I may ignore. - a new history is created each time I log in. I have to go to Saved History to get the last History I made. If I log multiple time, I get multiple empty unnamed History. Is there a way to see the last history when I open the session, or at least to get only one unnamed History ? I saw this post http://dev.list.galaxyproject.org/Unnamed-histories-td4655112.html. Has this ticket been treated ? Or does anyone manage to find another solution ? Thanks in advance, F.T

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RFC: new <action type="download_by_proxy">
by Björn Grüning 05 Jan '16

05 Jan '16

Hi Galaxy developers, this is a RFC to get the implementation details right for a new action type in `tool_dependencies.xml`. Since years we try to save a very crucial sustainability problem: **Non-sustainable links**! A little bit of history ------------------------ At first we tried to [mirror tarballs](https://github.com/bgruening/download_store) with sceptical sustainability, like BioC or random FTP servers. But over time we encountered many more places which we can not trust. Google-Code, SourceForge etc ... We tried to mirror the entire BioC history by tracking the SVN history down and creating tarball for every revision ... a Herculean task ... but still limited in scope because there are so many other things that needs to be archived to make Galaxy and all tools sustainable. In the end we ended up with the simplest solution, provide a community archive where everyone can drop tarballs that they want to be sustainable. The Galaxy Project was so generous and is funding the storage but we have plans to mirror and distribute the workload to universities and other institutes that want to help. The biggest problem we needed to solve was the access to the archive. Who can drop tarballs? How do we control access to prevent abuse of this system? We went ahead and the created the Cargo-Port: https://github.com/galaxyproject/cargo-port Access will be controlled by a community and via PR. Add your package and we will check the content (hopefully) automatically and the tarball will be mirrored to a storage server. RFC --- So far so good. This RFC is about the usage of Cargo-Port inside of Galaxy. I would like to propose a new action type that uses the Cargo-Port directly. It should replace `<action type="download_by_url" sha256sum="6387238383883...">` and `<action type="download_file">` and offer a more transparent and user-friendly solution. The current state of the art is quite cumbersome since we need to generate manually the checksum, offer the correct link and get the same information into Cargo-Port. I would like to streamline this a little bit and use this as a good opportunity to fix and work on https://github.com/galaxyproject/galaxy/issues/896. Proposal `<action type="download_by_proxy">`: * attribute for Id, Version, Platform, Architecture * no URL, no checksum * attribute for the URL to cargo-port/urls.tsv * default to the current github repo * configurable via galaxy.ini * this action will more or less trigger this curl command: `$ curl https://raw.githubusercontent.com/galaxyproject/cargo-port/master/gsl.py | python - --package_id augustus_3_1` * which give us the freedom to change API, columns ... in Cargo-Port without updating Galaxy core * the only API that need to keep stable is `gsl` * `gsl` will try to download from the original URL, specified in Cargo-Port. If this does not work we will download our archived one. * Changing the current working dir? Is this what we want, e.g. automatically uncompress and change cwd like `download_by_url`. * We will need an attribute to not uncompress. A few tools need the tarballs uncompressed. Single Point of Failure - a small remark ---------------------------------------- Previously, Galaxy packages relied entirely on the kindness of upstream to maintain existing packages indefinitely. Obviously not a sustainable practice. Every time a tarball was moved, we had to hope one of us retained a copy so that we could ensure reproducibility. With the advent of the Cargo Port, we now maintain a complete, redundant copy of every upstream tarball used in IUC and devteam repositories, additionally adding sha256sums for every file to ensure download integrity. The community is welcome to request that files they use in their packages be added as well. We believe this will help combat the single point of failure by providing at least one level of duplication. The Cargo Port is considering plans to provide mirrors of itself to various universities and another layer of redundancy. Thanks for reading and we appreciate any comments. Eric, Nitesh & Bjoern -- https://gist.github.com/bgruening/48297c27cd72cbadea7a

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January 2016 Galactic News
by Dave Clements 04 Jan '16

04 Jan '16

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security: brute force login
by Raphenya, Amogelang 04 Jan '16

04 Jan '16

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This job is waiting to run - Issue after Update to 15.10
by Matthias Enders 04 Jan '16

04 Jan '16

After some trying a college figured out, the Tools are working just fine, but all old datasets are not accessible by the tools via "redo the job". But I can Download them and so on.

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how to access current user's apikey
by rbrown1422＠comcast.net 04 Jan '16

04 Jan '16

Good morning team, Is there a way to access the current user's API Key similar to seeing their email address via a tool's xml parameter "$__user_email__" ? Thanks, Bob

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LDAP auth_conf.xml and search-filter condition
by Rémy Dernat 04 Jan '16

04 Jan '16

Hi list, I would like to enable a multiple search on (Open)LDAP to check if a user is also a member of a specific "galaxy" group. I did not find anything about this in the documentation. Indeed, we do not want that all the LDAP users to be able to login to galaxy and we do not want to change the LDAP structure because it is already used by many applications. I have a complex search-filter which is: <search-filter>(|(&(mail={email})(uid={username}))(&(cn=galaxy)(objectClass=posixGroup)(memberUid={username})))</search-filter> However, this search filter gave me two answers. It is normal because I am searching for the user, and then, if he belongs to a particular (posix)group. So the bind failed (because it needs only one answer). The basic one (to only bind) is working: <search-filter>(&(mail={email})(uid={username}))</search-filter> I also tried with 2 search-filter conditions but galaxy seems to keep only the last one. Is there any project to allow that in the (near) future versions (*) ? Or is there any hidden xml tag (not in documentation) which can permit to search the memberUid/memberOf value in LDAP ? In the meantime we will change the default quota (like just some bytes) for users to allow LDAP login (for all users already present in it). Best, Remy (*) Alternatively, what code should I change in Galaxy ? I would be happy to program it if I have enough time...

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Happy new year!
by Björn Grüning 04 Jan '16

04 Jan '16

Hi Galaxy Developers, last year was a blast for Galaxy and it seems that the Galaxy core team is preparing a new release soon with some big big features :) I really enjoy working with the Galaxy community and wish you all a happy new year. Let's keep rocking the Galaxy and make Bioinformatics even more accessible to everyone in 2016. Happy new year! Bjoern

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Re: [galaxy-dev] IPython and Rstudio are missing
by Mic 01 Jan '16

01 Jan '16

Hi all, Thank you for your email, I found on the bottom of this site https://wiki.galaxyproject.org/Admin/Config/nginxProxy a configuration for IE, but I am not quite sure whether it is enough. To update the documentation would be really awesome. Thank you in advance. Mic On Tue, Nov 17, 2015 at 12:05 AM, Björn Grüning <bjoern.gruening(a)gmail.com> wrote: > Nate configured it on Galaxy main last week, maybe I can convince him to > update the documentation ... > > > > Hi Mic, > > > > Yes... neither of us use Nginx as our primary proxy, so we never > > wrote the configuration for it. > > > > If you use Nginx I'm assuming you're familiar with its configuration. > > As you can see from the apache route, you really just need a few > > proxy_pass statements. If you can write those, we'd be more than > > happy to include them in our documentation. > > > > Ciao, Eric > > > > > > On 11/16/2015 07:44 AM, Mic wrote: > >> Hi all, Looking at this link > >> ( > http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html > ) > >> > >> > it seem Nginx configuration is missing. > >> > >> How to configure Nginx for IE and Galaxy 15.10? > >> > >> Thank you in advance. > >> > >> Mic > >> > >> On Thu, Nov 12, 2015 at 2:36 AM, Eric Rasche <esr(a)tamu.edu > >> <mailto:esr@tamu.edu>> wrote: > >> > >> Hi Mic, > >> > >> Replying off list as this seems to be a different set of issues > >> than others experience. > >> > >> 1) From your earlier mails it sounded like you had been reading > >> the docs on GIEs, but you asked for then here. Have you read > >> through > >> > http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html > >> > >> > yet? If so, how far did you get? > >> > >> 2) do you have docker installed? what version? ("docker -v" I > >> believe) > >> > >> 3) What release of Galaxy are you on? The instructions are version > >> specific in places. > >> > >> 3) All of the files for GIEs are in > >> config/plugins/interactive_environments. Have you made any changes > >> to your local ipython.ini or rstudio.ini? > >> > >> Any logs from GIEs will appear in your normal Galaxy logs. E.g. > >> paster.log > >> > >> Ciao, Eric > >> > >> 11. nov. 2015 10.05 a.m. skrev Mic <mictadlo(a)gmail.com > >> <mailto:mictadlo@gmail.com>>: > >> > >> Hi all, Is there any log files which could show what did go wrong > >> or is there any documentation how to install IEs? > >> > >> Thank you in advance. > >> > >> Mic > >> > >> On Mon, Nov 9, 2015 at 9:12 AM, Mic <mictadlo(a)gmail.com > >> <mailto:mictadlo@gmail.com>> wrote: > >> > >> Hi Bjoern, Thank you for your email. I tried the attached Annovar > >> output which is tabular separated. Unfortunately, Rstudio and > >> Ipython still did not show up. > >> > >> Thank you in advance. > >> > >> Best wishes, > >> > >> Mic > >> > >> On Sat, Nov 7, 2015 at 9:58 AM, Björn Grüning > >> <bjoern.gruening(a)gmail.com <mailto:bjoern.gruening@gmail.com>> > >> wrote: > >> > >> Hi Mic, > >> > >> please check any other file than a VCF file. Try a txt file for > >> example. > >> > >> Thanks, Bjoern > >> > >> Am 07.11.2015 um 00:54 schrieb Mic: > >>> Hi Eric, I added your line to ipython.xml and rstudio.xml and > >> restarted Galaxy, but > >>> still Rstudio and Ipython do not appear on my test.vcf > >> file by clicking the > >>> *visualize* icon. > >>> > >>> <test type="isinstance" test_attr="datatype" > >>> result_type="datatype">tabular.Tabular</test> <test > >>> type="isinstance" test_attr="datatype" > >>> result_type="datatype">data.Text</test> *<test type="isinstance" > >>> test_attr="datatype" result_type="datatype">tabular.VCF</test>* > >>> > >>> What did I miss? > >>> > >>> Thank you in advance. > >>> > >>> Mic > >>> > >>> On Sat, Nov 7, 2015 at 1:13 AM, Eric Rasche > >> <esr(a)tamu.edu <mailto:esr@tamu.edu>> wrote: > >>> > >>>> Hi Mic, > >>>> > >>>> I don't believe GIEs are currently activated for > >> anything other than plain > >>>> text and tabular files. You can edit the > >>>> > >> > $GALAXY_ROOT/config/plugins/interactive_environments/ipython/config/ipython.xml > >> > >> (and rstudio/config/rstudio.xml) files to add a line like: > >>>> > >>>> Konsole output <test type="isinstance" test_attr="datatype" > >>>> result_type="datatype">tabular.VCF</test> > >>>> > >>>> and that /should/ let you open VCF files. (I haven't > >> tested that exact > >>>> datatype but I believe that should work). GIEs have > >> been somewhat > >>>> experimental so far, so we haven't felt the need to > >> expand which datatypes > >>>> they apply to lest we overwhelm/surprise users. > >>>> > >>>> Ciao, Eric > >>>> > >>>> > >>>> > >>>> > >>>> On 11/06/2015 02:56 AM, Mic wrote: > >>>>> Hello, Last week, I cloned Galaxy from Github. I uploaded a > >> VCF file from my > >>>>> computer. I also installed the following additional > >> software: > >>>>> > >>>>> /apt-key adv --keyserver keyserver.ubuntu.com > >> <http://keyserver.ubuntu.com> > >>>>> <http://keyserver.ubuntu.com> --recv-keys E084DAB9/ /echo > >>>>> 'deb > >> http://cran.r-project.org/bin/linux/ubuntu trusty/' >> > >>>>> /etc/apt/sources.list/ /apt-get -qq update && apt-get > >>>>> install > >> --no-install-recommends -y > >>>>> libcurl4-openssl-dev libxml2-dev/ /apt-get install > >>>>> apt-transport-https python-dev > >> libc-dev pandoc > >>>>> pkg-config liblzma-dev libbz2-dev libpcre3-dev/ /apt-get > >>>>> install libblas-dev liblapack-dev gfortran > >> libzmq3-dev curl/ > >>>>> /apt-get install libfreetype6-dev libpng-dev > >> net-tools procps r-base > >>>>> libreadline-dev / /pip install distribute --upgrade/ /pip > >>>>> install scipy sklearn-pandas bioblend > >> matplotlib patsy pysam khmer > >>>>> ggplot mpld3 sympy rpy2/ /pip install pyzmq ipython==2.4 > >>>>> jinja2 tornado > >> pygments numpy biopython > >>>>> scikit-learn pandas/ > >>>>> > >>>>> However, clicking the /visualize/ icon no iPython > >> and RStudio are > >>>>> visible. Galaxy is in my home folder installed > >> //home/lorencm/galaxy./ > >>>>> > >>>>> What am I missing? > >>>>> > >>>>> Thank you in advance. > >>>>> > >>>>> Mic > >>>>> > >>>>> > >>>>> > >> ___________________________________________________________ > >>>>> 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/ > >>>>> > >>>> > >>>> -- Eric Rasche Programmer II > >>>> > >>>> Center for Phage Technology Rm 312A, BioBio Texas A&M > >>>> University College Station, TX 77843 404-692-2048 > >>>> <tel:404-692-2048> esr(a)tamu.edu <mailto:esr@tamu.edu> > >>>> > >>>> > >>> > >>> > >>> > >>> > >> ___________________________________________________________ > >>> 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/ > >>> > >> > >> > >> > >> > > >

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Tool Release Announcement: JBrowse-in-Galaxy v0.4
by Eric Rasche 01 Jan '16

01 Jan '16

Howdy Galaxy devs, A quick tool release announcement to ring in the new year. The latest version of the JBrowse-in-Galaxy tool is now available! https://toolshed.g2.bx.psu.edu/view/iuc/jbrowse/7342f467507b This tool was discussed in a lightning talk at GCC2015 but would not install nicely due to a broken dependency chain. This has since been fixed and many features added in the latest version: * Support for dataset collections * Support for multiple contigs/genomes within the JBrowse instance * Excessive configuration options for controlling colouring of tracks * Removed interstitial, open JBrowse in the main panel with one click. * Support for translation tables other than table 1. More details in the pull request <https://github.com/galaxyproject/tools-iuc/pull/507> for the curious. And a silly image to top it off :) Ciao, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu

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galaxy-dev January 2016