[galaxy-dev] Error on chemfp version 1.1p1 installation
Hi all, I'm trying install chemical toolbox on a local instance and I got an error the following error raised by chemfp dependency: File "/home/leobiscassi/programs/galaxy-local/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/home/leobiscassi/programs/galaxy-local/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 181, in url_download raise Exception( err_msg ) Error downloading from URL http://chem-fingerprints.googlecode.com/files/chemfp-1.1p1.tar.gz: HTTP Error 404: Not Found This link is the same it's in cargo-port [1], but isn't working, can you help me? [1] https://github.com/galaxyproject/cargo-port/blob/master/urls.tsv#L396 -- Best regards, *Léo Biscassi* ___ 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] Tool needs a particular file extension
Hi Steve, try do like this example [1]
[1]
https://github.com/leobiscassi/autodock_vina_tools/blob/dev/tools/prepare_ligand/prepare_ligand.xml
Cheers,
On Fri, Oct 21, 2016 at 2:48 PM Steve Cassidy
wrote:
> Hi,
> I’m wrapping a tool that needs it’s input to have a known file extension
> (an audio file, eg. .wav). Since Galaxy stores all data as .dat files the
> tool is falling over since it doesn’t know what .dat is.
>
> I thought I’d be able to get around this by hard linking the .dat file to
> the same name with a .wav extension (dataset_1.dat.wav), this works when I
> try it with the tool on the command line but within Galaxy it fails, here’s
> my :
>
> ln $signal* ${signal}.wav* &
> /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language
> BPF=$bpf INSKANTEXTGRID=$inskantextgrid
> INSORTTEXTGRID=$insorttextgrid
> MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen
> WEIGHT=$weight
> INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence
> OUTSYMBOL=$outsymbol
> OUT=$output *SIGNAL=${signal}.wav*
>
> resulting in the job command line:
>
> ln /tmp/tmp7AZvx7/files/000/dataset_2.dat
> */tmp/tmp7AZvx7/files/000/dataset_2.dat.wav* &
> /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=aus
> BPF=/tmp/tmp7AZvx7/files/000/dataset_1.dat
> INSKANTEXTGRID=false INSORTTEXTGRID=false MODUS=standard MAUSSHIFT=10
> MINPAUSLEN=5 WEIGHT=7.0 INSPROB=0.0
> NOINITIALFINALSILENCE=no OUTSYMBOL=sampa
> OUT=/tmp/tmp7AZvx7/files/000/dataset_3.dat SIGNAL=
> */tmp/tmp7AZvx7/files/000/dataset_2.dat.wav*
>
> I’m getting an error message from the tool:
>
>
> *sox FAIL formats: can't open input file
> `/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav': WAVE: RIFF header not found *
> this suggests that the hard link didn’t get made. I tried copying the
> file instead but got the same result.
>
> I could go in and patch the tool script to be more forgiving but it would
> be good to find a solution that didn’t require that if possible.
>
> Any pointers appreciated.
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> ___
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--
Best regards,
*Léo Biscassi*
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Re: [galaxy-dev] Galaxy Proteomics Hackathon
I don't know anything about GalaxyP, but I think I can help a little bit with conda packages, if that works for you I can join to hackathon. Best regards On Fri, Sep 9, 2016 at 12:01 PM Björn Grüning wrote: > Hi all! > > I would like to spread the news from the GalaxyP team about a new > hackthon. Please join and help us if you have some time! > > > * > > The first Galaxy-P CONDA hackathon will be held on September 27th and 28th. > Galaxy-P and proteomics tool developers will participate in this > hackathon to "CONDA-package" some of the prioritized proteomics tools > within Galaxy. The hackathon will be an online event which will start > with an introduction to Galaxy structure and CONDA packaging by Bjoern > Gruening. > > https://github.com/galaxyproteomics/tools-galaxyp/issues/57 > > Details soon. Please see if you would like to publicize this. > > Thanks and Regards, > Pratik > ___ > 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/ -- Best regards, *Léo Biscassi* ___ 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] Problem with conda on galaxy 16.07
Hi folks,
Today after perform some tests with conda on galaxy 16.07 the follow
message was returned in my terminal:
"*Conda dependency seemingly installed but failed to build job environment.*
"
The error occurs when *build_isolated_environment()* function is call.
Below some variable values:
*is_installed* = *True*
*job_directory* = */home/leobiscassi/programs/galaxy/job_work_dir/000/17*
*env_path* =
*/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env*
*exit_code* = *127*
Analyzing inside of the *build_isolated_environment()*, the
*exec_create() *function
is executed because *path* variable (
*/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env*) don't
exists, the command executed by *exec_create* is showed below:
*deps/_conda/bin/conda create -y --unknown --offline --prefix
/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env --file
./database/tmp/jobdepsIGslWfe2bd2345d2ec1bb4aeb81211183570bae7db28a3bea4f7ff9e8e75074719a7ee/__mgltools@1.5.6
> /dev/null*
Some important values:
*env* = *{'HOME': 'deps/_conda', 'CONDARC':
'/home/leobiscassi/programs/galaxy/deps/_condarc'}*
The command return is '*/bin/sh: 1: deps/_conda/bin/conda: not found*', but
the binary exist. Anyone can help me with this?
Thanks in advance.
--
Best regards,
*Léo Biscassi*
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Re: [galaxy-dev] Introducing Conda as a new standard for Galaxy tool dependencies
Hi Bjorn, I read the documentation about conda shared early in this email and I have one more question: If I already a conda installation on computer and don't wish share this installation to control galaxy dependencies, galaxy works fine with your own conda auto installation or I have pay attention in more some detail? On Mon, Aug 29, 2016 at 5:37 AM Peter Cock wrote: > That's great Bjoern, > > I was thinking we should mention this on the wiki (with a link > to the documentation rather than duplicating it). There are > some existing pages about the tool_dependencies.xml > system - but no obvious top level introduction that I saw? > > https://wiki.galaxyproject.org/ToolDependencyRecipes > https://wiki.galaxyproject.org/ToolShed/PackageRecipes > https://wiki.galaxyproject.org/ToolDependenciesTagSets > https://wiki.galaxyproject.org/ToolsWithDependenciesInSeparateRepositories > > Where on the wiki do people think would be best? > > Peter > > On Sun, Aug 28, 2016 at 9:41 PM, Léo Biscassi > wrote: > > Nice job! I was really anxious for some documentation about this theme! > > Thanks all involved! > > > > On Fri, Aug 26, 2016 at 3:38 PM Björn Grüning > > > wrote: > >> > >> Hi all, > >> > >> Galaxy 16.07 was just released: > >> https://docs.galaxyproject.org/en/master/releases/16.07_announce.html > >> and the IUC has some news to share with you. > >> > >> For a more readable version please see: > >> https://docs.galaxyproject.org/en/master/admin/conda_faq.html > >> > >> > >> > >> Galaxy tools (also called wrappers) traditionally use Tool Shed package > >> recipes to install their dependencies. At the tool’s installation time > >> the recipe is downloaded and executed in order to provide the underlying > >> software executables. Introduction of these Galaxy-specific recipes was > >> a necessary step at the time, however nowadays there are other more > >> mature and stable options to install software in a similar manner. The > >> Galaxy community has taken steps to improve the tool dependency system > >> in order to enable new features and expand its reach. This document aims > >> to describe these and answer the FAQ. > >> > >> It is a pleasure to announce the adoption of a new standard for tool > >> dependencies in Galaxy which has been integrated over the last six > >> months: Conda packages! > >> Not only do Conda packages make tool dependencies more reliable and > >> stable, they are also easier to test and faster to develop than the > >> traditional Tool Shed package recipes . > >> > >> Conda is a package manager like apt-get, yum, pip, brew or guix. We > >> don’t want to argue about the relative merits of various package > >> managers here, in fact Galaxy supports multiple package managers and we > >> welcome community contributions (such as implementing a Guix package > >> manager or enhancing the existing brew support to bring it on par with > >> Conda). > >> > >> As a community, we have decided that Conda is the one that best fulfills > >> our needs. The following are some of the crucial Conda features that led > >> to this decision: > >> > >> * Installation of packages does not require root privileges > >> (Installation at any location the Galaxy user has write access to) > >> * Multiple versions of software can be installed in parallel > >> * HPC-ready > >> * Faster and more robust package installations through pre-compiled > >> packages (no build environment complications) > >> * Independent of programming language (R, Perl, Python, Julia, Java, > >> pre-compiled binaries, and more) > >> * Easy to write recipes (1 YAML description file + 1 Bash install > script) > >> * An active, large and growing community (with more and more software > >> authors managing their own recipes) > >> * Extensive documentation: Conda documentation > >> (http://conda.pydata.org/docs/building/build.html) and Conda > quick-start > >> (http://conda.pydata.org/docs/get-started.html) > >> > >> Below we answer some common questions (collected by Lance Parsons): > >> > >> 1. How do I enable Conda dependency resolution for existing Galaxy > >> installations? > >> --- > >> > >> Most Galaxy administrators have not set up a dependency resolvers > >> configuration file (dependency_resolvers_co
Re: [galaxy-dev] Introducing Conda as a new standard for Galaxy tool dependencies
> There is currently a limitation in the way conda packages are being > built. This limitation will be addressed shortly by the Conda community, > however this requires all packages to be rebuilt. > To work around this limitation, please make sure that the total length > of the conda_prefix and job_working_directory path is less than 50 > characters long. > If this is your problem, you should see a warning similar to the > following in your galaxy log files: > ERROR: placeholder > > '/home/ray/r_3_3_1-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_pl' > too short > In rare cases conda may not have been properly installed by galaxy. A > symptom for this is if there is no activate script in conda_prefix/bin. > In that case you can delete the conda_prefix folder and restart galaxy, > which will again attempt to install conda. > > If this does not solve your problem or you have any trouble following > the instructions, please ask on the galaxy mailing list or the galaxy > IRC channel. > > > --- > One last thing that is important to me: the entire Galaxy-Conda project > is an amazing community effort - not only within the Galaxy community, > but we team up with the Conda community as well, in particular with the > BioConda folks. Thanks to Johannes Köster, Ryan Dale and the entire > community around this package manager which have created around 1500 > bioinformatics packages just in the last year. > > Thanks to John Chilton who has written the Galaxy Conda integration last > December and is pushing tool development in Galaxy to a new level. Many > thanks to Nicola Soranzo for his constant support and reviews in all > mentioned projects, he is everywhere to help - you will see! Thanks also > to Peter van Heusden, Marius van den Beek and Brad Langhorst – they have > worked hard on Conda-Galaxy Integration to make it shine in 16.07. I > want to thank Lance Parsons for his questions that inspired me to write > this down and his constant support in making tools better in Galaxy – > Lance I hope with Conda you will have less pain with dependencies in > general! > > Last but not least I would like to thank the entire IUC and the over 50 > IUC contributors that have migrated most of the IUC tools to Conda > packages over the last 6 months. > > You all did a truly amazing work here – and I‘m sure it will benefit the > tool development in Galaxy tremendously. > > Enjoy Galaxy + Conda, > Björn, on behalf of the IUC > > P.S. As soon as you have a Conda package, we have a system for you to > generate Docker containers out of it: https://github.com/mulled/mulled. > These containers can than be used by Galaxy to resolve dependencies as > well, if you prefer Docker containers over Conda packages. > ___ > 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/ -- Best regards, *Léo Biscassi* ___ 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] Information about SparkGalaxy
Hi folks, I recently saw this tweet [1] about SparkGalaxy. I'm working in one project which uses spark to process protein-ligand docking data and would like try use this workflow in my project, can anyone give me more information, e.g. where I can download it or if it's built in galaxy implementation, about? I'm pretty excited, this is a great job! [1] https://twitter.com/galaxyproject/status/758727733643874304 Thanks for your attention! -- Best regards, *Léo Biscassi* ___ 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] Auto detection of output format Galaxy custom tool
Hi Katherine, The file datatype have support on galaxy plataform!? If not, you add the datatype what you need in your galaxy instance!? Att. On Wed, Jun 29, 2016, 11:16 AM Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > Hi everyone, > I am looking to auto-detect the file format of a file outputted by a > python tool I have written. Does anyone have any idea how to do this? I > have tried setting the format attribute to "auto" with no luck. Let me know > if you would like to see my tool config file. > Cheers, > Katherine > ___ > 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/ -- Best regards, *Léo Biscassi* ___ 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] Doubts about Galaxy installation.
ah ... one observation, the mercurial was substituted for git. If you need help I can help you in portuguese, send me one email. Att. On Mon, Jun 27, 2016 at 3:24 PM Léo Biscassi wrote: > Hi Álvaro, welcome to the galaxy community! Brazilian guy here too! :) > I made this post in portuguese [1] with the basic instructions to install > your own galaxy instance for tests in a notebook. Your machine > configuration is enough to run and make tests with galaxy! > > [1] > https://biscassi.wordpress.com/2015/02/09/instalando-um-servidor-do-galaxy-project-1/ > > Att. > > On Mon, Jun 27, 2016 at 3:19 PM Álvaro Rios > wrote: > >> Dear Member of the Galaxy Team, >> >> >> >> My name is Álvaro Rios, I am Associate Professor of the North Fluminense >> State University, RJ, Brazil. I am a beginner in the use of Galaxy tools >> and, I would like to install my own Galaxy. >> >> However I am not familiarized with command lines for instation of Galaxy. >> My interest is to use tool like BS-seeker2 avaible into Toolshed. I am >> using a MacBook Pro (2,2 GHz Intel Core i7; 16G RAM). It is enough to work >> with Galaxy? >> >> I saw that I can download a zipped file version and install it. What file >> I need to click to install Galaxy? >> >> How can I become a administrador? >> >> Thank you for your attention, >> >> With Best Regards >> >> Álvaro Rios. >> ___ >> 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/ > > -- > Best regards, > *Léo Biscassi* > -- Best regards, *Léo Biscassi* ___ 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] Doubts about Galaxy installation.
Hi Álvaro, welcome to the galaxy community! Brazilian guy here too! :) I made this post in portuguese [1] with the basic instructions to install your own galaxy instance for tests in a notebook. Your machine configuration is enough to run and make tests with galaxy! [1] https://biscassi.wordpress.com/2015/02/09/instalando-um-servidor-do-galaxy-project-1/ Att. On Mon, Jun 27, 2016 at 3:19 PM Álvaro Rios wrote: > Dear Member of the Galaxy Team, > > > > My name is Álvaro Rios, I am Associate Professor of the North Fluminense > State University, RJ, Brazil. I am a beginner in the use of Galaxy tools > and, I would like to install my own Galaxy. > > However I am not familiarized with command lines for instation of Galaxy. > My interest is to use tool like BS-seeker2 avaible into Toolshed. I am > using a MacBook Pro (2,2 GHz Intel Core i7; 16G RAM). It is enough to work > with Galaxy? > > I saw that I can download a zipped file version and install it. What file > I need to click to install Galaxy? > > How can I become a administrador? > > Thank you for your attention, > > With Best Regards > > Álvaro Rios. > ___ > 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/ -- Best regards, *Léo Biscassi* ___ 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] Galaxy tools for docking protein-compounds.
Hi, thanks for the considerations in the code, I'll make the changes later. The packages Autodock Vina and MGL Tools works fine!? I saw that tests passed with success on Travis. Cheers, On Tue, Mar 15, 2016 at 4:50 AM Bjoern Gruening wrote: > Saw it! Will review it today, this looks really nice! > > > On 15.03.2016 08:28, Léo Biscassi wrote: > > Hi Bjorn, I've created the pull request [1] in your repository. I will be > grateful if you can assist me with the functional tests on the docking tool > and the final validation of the tool dependencies. > > [1] https://github.com/bgruening/galaxytools/pull/310 > > Thanks a lot! > > Best regards, > > On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi > wrote: > >> Hi, thanks for the reply. >> About the branch model, ok! I'll follow the model presented. >> About the error in planemo functional tests, the problem is that the >> content of example output is not the same of output file of test. This is >> shown by the command diff performed on planemo test. >> Today, I'll create a pull request in your repository for that we can fix >> the problem. >> Thank for the helps. >> >> I'm excited about this. >> >> Best regards, >> >> >> >> On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning >> wrote: >> >>> >>> >>> Am 10.03.2016 um 21:30 schrieb Léo Biscassi: >>> > Hi folks, >>> > I have make somes alterations on my tools to adjust of according with >>> > best pratices of development of tools presented in [1] [2]. The >>> > repository of tools was changed for [3]. >>> > I was testing the tool of docking [4] with the command planemo t, but >>> as >>> > the algorithm used is heuristic, the output files not have the same >>> > content that as output files example and planemo tests fails. Any >>> > suggestion to solve this problem? >>> >>> Is there anything in the file that is the same? Filesize? Some lines >>> that are everytime the same (no matter where in the file)? >>> >>> You could create a PR and I will review it and give you feedback. >>> Cheers, >>> Bjoern >>> >>> >>> > [1] >>> > >>> https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html >>> > [2] https://planemo.readthedocs.org/en/latest/ >>> > [3] https://github.com/leobiscassi/autodock_vina_tools >>> > [4] >>> > >>> https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking >>> > >>> > Att. >>> > >>> > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi >> > <mailto:leo.bisca...@gmail.com>> wrote: >>> > >>> > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented >>> > in [1]? Could guide me about it? >>> > >>> > [1] >>> https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md >>> > >>> > Att. >>> > >>> > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi < >>> leo.bisca...@gmail.com >>> > <mailto:leo.bisca...@gmail.com>> wrote: >>> > >>> > Ok, thanks! >>> > >>> > Best regards, >>> > >>> > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning >>> > mailto:bjoern.gruen...@gmail.com>> >>> > wrote: >>> > >>> > >>> > >>> > Am 28.12.2015 um 20:33 schrieb Léo Biscassi: >>> > > Hi, >>> > > Thanks all your attention. >>> > > Although my project is functional prototype, its current >>> > version is able to >>> > > integrate with projects. In fact, I was looking for >>> > projects like >>> > > ChemicalToolBoX because I would like to develop my tools >>> > under project that >>> > > has more options. In this way, ChemicalToolBoX is a great >>> > opportunity for >>> > > me. >>> > > Can you update the trello card with my project? Is it >>> > necessary for your >>> > > organization? >>> > >>> > I added you :) So you have all right to modify cards. >>> > Let me know
Re: [galaxy-dev] Galaxy tools for docking protein-compounds.
Hi Bjorn, I've created the pull request [1] in your repository. I will be grateful if you can assist me with the functional tests on the docking tool and the final validation of the tool dependencies. [1] https://github.com/bgruening/galaxytools/pull/310 Thanks a lot! Best regards, On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi wrote: > Hi, thanks for the reply. > About the branch model, ok! I'll follow the model presented. > About the error in planemo functional tests, the problem is that the > content of example output is not the same of output file of test. This is > shown by the command diff performed on planemo test. > Today, I'll create a pull request in your repository for that we can fix > the problem. > Thank for the helps. > > I'm excited about this. > > Best regards, > > > > On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning > wrote: > >> >> >> Am 10.03.2016 um 21:30 schrieb Léo Biscassi: >> > Hi folks, >> > I have make somes alterations on my tools to adjust of according with >> > best pratices of development of tools presented in [1] [2]. The >> > repository of tools was changed for [3]. >> > I was testing the tool of docking [4] with the command planemo t, but as >> > the algorithm used is heuristic, the output files not have the same >> > content that as output files example and planemo tests fails. Any >> > suggestion to solve this problem? >> >> Is there anything in the file that is the same? Filesize? Some lines >> that are everytime the same (no matter where in the file)? >> >> You could create a PR and I will review it and give you feedback. >> Cheers, >> Bjoern >> >> >> > [1] >> > >> https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html >> > [2] https://planemo.readthedocs.org/en/latest/ >> > [3] https://github.com/leobiscassi/autodock_vina_tools >> > [4] >> > >> https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking >> > >> > Att. >> > >> > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi > > <mailto:leo.bisca...@gmail.com>> wrote: >> > >> > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented >> > in [1]? Could guide me about it? >> > >> > [1] >> https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md >> > >> > Att. >> > >> > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi < >> leo.bisca...@gmail.com >> > <mailto:leo.bisca...@gmail.com>> wrote: >> > >> > Ok, thanks! >> > >> > Best regards, >> > >> > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning >> > mailto:bjoern.gruen...@gmail.com>> >> > wrote: >> > >> > >> > >> > Am 28.12.2015 um 20:33 schrieb Léo Biscassi: >> > > Hi, >> > > Thanks all your attention. >> > > Although my project is functional prototype, its current >> > version is able to >> > > integrate with projects. In fact, I was looking for >> > projects like >> > > ChemicalToolBoX because I would like to develop my tools >> > under project that >> > > has more options. In this way, ChemicalToolBoX is a great >> > opportunity for >> > > me. >> > > Can you update the trello card with my project? Is it >> > necessary for your >> > > organization? >> > >> > I added you :) So you have all right to modify cards. >> > Let me know if you need help with Tool development or git. >> > >> > This is exciting! >> > Cheers, >> > Bjoern >> > >> > > Best regards, >> > > >> > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning >> > > bjoern.gruen...@gmail.com>> >> > > wrote: >> > > >> > >> >> > >> >> > >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi: >> > >>> Hi, >> > >>> >> > >>> I've found this Trello card ( >> > >&g
Re: [galaxy-dev] Galaxy tools for docking protein-compounds.
Hi, thanks for the reply. About the branch model, ok! I'll follow the model presented. About the error in planemo functional tests, the problem is that the content of example output is not the same of output file of test. This is shown by the command diff performed on planemo test. Today, I'll create a pull request in your repository for that we can fix the problem. Thank for the helps. I'm excited about this. Best regards, On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning wrote: > > > Am 10.03.2016 um 21:30 schrieb Léo Biscassi: > > Hi folks, > > I have make somes alterations on my tools to adjust of according with > > best pratices of development of tools presented in [1] [2]. The > > repository of tools was changed for [3]. > > I was testing the tool of docking [4] with the command planemo t, but as > > the algorithm used is heuristic, the output files not have the same > > content that as output files example and planemo tests fails. Any > > suggestion to solve this problem? > > Is there anything in the file that is the same? Filesize? Some lines > that are everytime the same (no matter where in the file)? > > You could create a PR and I will review it and give you feedback. > Cheers, > Bjoern > > > > [1] > > > https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html > > [2] https://planemo.readthedocs.org/en/latest/ > > [3] https://github.com/leobiscassi/autodock_vina_tools > > [4] > > > https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking > > > > Att. > > > > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi > <mailto:leo.bisca...@gmail.com>> wrote: > > > > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented > > in [1]? Could guide me about it? > > > > [1] https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md > > > > Att. > > > > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi > <mailto:leo.bisca...@gmail.com>> wrote: > > > > Ok, thanks! > > > > Best regards, > > > > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning > > mailto:bjoern.gruen...@gmail.com>> > > wrote: > > > > > > > > Am 28.12.2015 um 20:33 schrieb Léo Biscassi: > > > Hi, > > > Thanks all your attention. > > > Although my project is functional prototype, its current > > version is able to > > > integrate with projects. In fact, I was looking for > > projects like > > > ChemicalToolBoX because I would like to develop my tools > > under project that > > > has more options. In this way, ChemicalToolBoX is a great > > opportunity for > > > me. > > > Can you update the trello card with my project? Is it > > necessary for your > > > organization? > > > > I added you :) So you have all right to modify cards. > > Let me know if you need help with Tool development or git. > > > > This is exciting! > > Cheers, > > Bjoern > > > > > Best regards, > > > > > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning > > mailto:bjoern.gruen...@gmail.com > >> > > > wrote: > > > > > >> > > >> > > >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi: > > >>> Hi, > > >>> > > >>> I've found this Trello card ( > > >>> https://trello.com/c/2eIu6SBa/49-autodock-integration). > > Do you have more > > >>> information about it? > > >> > > >> Afaik we can not use his work as it was done for some > > company and he > > >> moved on ... so this is unfortunately no option afaik. > > >> > > >> > > >> > > >>> best, > > >>> > > >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning > > mailto:bjoern.gruen...@gmail.com > > > > >>> > > >>> wrote: > >
Re: [galaxy-dev] Galaxy tools for docking protein-compounds.
Hi folks, I have make somes alterations on my tools to adjust of according with best pratices of development of tools presented in [1] [2]. The repository of tools was changed for [3]. I was testing the tool of docking [4] with the command planemo t, but as the algorithm used is heuristic, the output files not have the same content that as output files example and planemo tests fails. Any suggestion to solve this problem? [1] https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html [2] https://planemo.readthedocs.org/en/latest/ [3] https://github.com/leobiscassi/autodock_vina_tools [4] https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking Att. On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi wrote: > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented in > [1]? Could guide me about it? > > [1] https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md > > Att. > > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi > wrote: > >> Ok, thanks! >> >> Best regards, >> >> On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning >> wrote: >> >>> >>> >>> Am 28.12.2015 um 20:33 schrieb Léo Biscassi: >>> > Hi, >>> > Thanks all your attention. >>> > Although my project is functional prototype, its current version is >>> able to >>> > integrate with projects. In fact, I was looking for projects like >>> > ChemicalToolBoX because I would like to develop my tools under project >>> that >>> > has more options. In this way, ChemicalToolBoX is a great opportunity >>> for >>> > me. >>> > Can you update the trello card with my project? Is it necessary for >>> your >>> > organization? >>> >>> I added you :) So you have all right to modify cards. >>> Let me know if you need help with Tool development or git. >>> >>> This is exciting! >>> Cheers, >>> Bjoern >>> >>> > Best regards, >>> > >>> > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning < >>> bjoern.gruen...@gmail.com> >>> > wrote: >>> > >>> >> >>> >> >>> >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi: >>> >>> Hi, >>> >>> >>> >>> I've found this Trello card ( >>> >>> https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have >>> more >>> >>> information about it? >>> >> >>> >> Afaik we can not use his work as it was done for some company and he >>> >> moved on ... so this is unfortunately no option afaik. >>> >> >>> >> >>> >> >>> >>> best, >>> >>> >>> >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning < >>> bjoern.gruen...@gmail.com >>> >>> >>> >>> wrote: >>> >>> >>> >>>> Hi, >>> >>>> >>> >>>> yes we had some idea, but nothing materialised so far. We started >>> with >>> >>>> the visualisation, because this was more fun :) >>> >>>> >>> >>>> Have a look at this board for more ideas: >>> >>>> https://trello.com/b/t9Wr8lSY/chemicaltoolbox >>> >>>> >>> >>>> Ciao, >>> >>>> Bjoern >>> >>>> >>> >>>> >>> >>>> Am 28.12.2015 um 19:29 schrieb Léo Biscassi: >>> >>>>> Hi Bjorn, thanks for reply. >>> >>>>> Would be great idea join forces in this project. How do you plan >>> extend >>> >>>>> ChemicalToolBoX with docking? I would like to know more details. >>> >>>>> >>> >>>>> Att. >>> >>>>> >>> >>>>> On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning < >>> >> bjoern.gruen...@gmail.com >>> >>>>> >>> >>>>> wrote: >>> >>>>> >>> >>>>>> Hi Léo, >>> >>>>>> >>> >>>>>> idneed we have a small community that is bringing Cheminformatics >>> into >>> >>>>>> the Galaxy. It's called ChemicalToolBox and is located here: >>> >>>>>> >>> >>>>>> >>> https://github.com/bgruening/galaxytools/tree/mast
Re: [galaxy-dev] Problems with planemo functional tests
Hi Gildas, thanks for the reply. I had renamed galaxy.ini.sample file to galaxy.ini and performed my configurations to the server. In fact, I created the file galaxy.ini.sample and command works fine! Thanks a lot! Best regards, On Thu, Mar 3, 2016 at 5:46 AM Gildas Le Corguillé < lecorgui...@sb-roscoff.fr> wrote: > Hi, > > Do you still have the config/galaxy.ini.sample file unchanged ? > > We observed this message when some .sample are missing or were modified. > > Gildas > > - > Gildas Le Corguillé - Bioinformatician/Bioanalyste > > Plateform ABiMS (Analyses and Bioinformatics for Marine Science) > http://abims.sb-roscoff.fr > > Member of the Workflow4Metabolomics project > http://workflow4metabolomics.org > > Station Biologique de Roscoff - UPMC/CNRS - FR2424 > Place Georges Teissier 29680 Roscoff FRANCE > tel: +33 2 98 29 23 81 > ------ > > > > Le 3 mars 2016 à 07:31, Léo Biscassi a écrit : > > Hi, the command that you suggested not working, the same output is > presented. I tested with the following commands: > > *sudo planemo test > /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml > --galaxy_root=/home/leobiscassi/programs/galaxy* > > *sudo planemo test > /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml* > > What is the influence of xUnit file in the process? I did the question > because the warning message showing "*Cannot locate xUnit report option > for tests - update Galaxy for more detailed breakdown*". > > P.S.: My Galaxy instance is the latest stable version. > > Best regards, > > On Thu, Mar 3, 2016 at 2:53 AM Björn Grüning > wrote: > >> Hi, >> >> maybe I'm mistaken something, its way to early here ... but you need to >> specify a path to the tool you want to test. >> >> For example: >> >> planemo test /foo/bar/foo.xml >> >> or to a directory full of tools. >> >> planemo test /foo/bar >> >> Hope this helps, >> Bjoern >> >> Am 03.03.2016 um 04:48 schrieb Léo Biscassi: >> > Hi Folks, >> > I tried follow this tutorial [1], but I have problems in execute the >> > command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for >> > perform functional tests, any suggestion? >> > Bellow some images about this problem: >> > >> > imagem1.jpg >> > *Figure 1: *Command >> > >> > imagem2.jpg >> > *Figure 2:* Error >> > >> > imagem3.jpg >> > *Figure 3: *Galaxy Path >> > >> > Planemo's version is 0.23.0. >> > >> > [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html >> > >> > P.S: The command is utilized for same tool presented in tutorial. >> > >> > Att. >> > -- >> > *Léo Biscassi* >> > Facebook - https://pt-br.facebook.com/lbiscassi >> > Linkedin - https://br.linkedin.com/in/leobiscassi >> > Skype - biscassi.leo >> > Twitter - https://twitter.com/leobiscassi >> > >> > >> > ___ >> > 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/ >> > >> > -- > *Léo Biscassi* > Facebook - https://pt-br.facebook.com/lbiscassi > Linkedin - https://br.linkedin.com/in/leobiscassi > Skype - biscassi.leo > Twitter - https://twitter.com/leobiscassi > ___ > 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/ > > > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___ 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] Problems with planemo functional tests
Hi, the command that you suggested not working, the same output is presented. I tested with the following commands: *sudo planemo test /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml --galaxy_root=/home/leobiscassi/programs/galaxy* *sudo planemo test /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml* What is the influence of xUnit file in the process? I did the question because the warning message showing "*Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown*". P.S.: My Galaxy instance is the latest stable version. Best regards, On Thu, Mar 3, 2016 at 2:53 AM Björn Grüning wrote: > Hi, > > maybe I'm mistaken something, its way to early here ... but you need to > specify a path to the tool you want to test. > > For example: > > planemo test /foo/bar/foo.xml > > or to a directory full of tools. > > planemo test /foo/bar > > Hope this helps, > Bjoern > > Am 03.03.2016 um 04:48 schrieb Léo Biscassi: > > Hi Folks, > > I tried follow this tutorial [1], but I have problems in execute the > > command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for > > perform functional tests, any suggestion? > > Bellow some images about this problem: > > > > imagem1.jpg > > *Figure 1: *Command > > > > imagem2.jpg > > *Figure 2:* Error > > > > imagem3.jpg > > *Figure 3: *Galaxy Path > > > > Planemo's version is 0.23.0. > > > > [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html > > > > P.S: The command is utilized for same tool presented in tutorial. > > > > Att. > > -- > > *Léo Biscassi* > > Facebook - https://pt-br.facebook.com/lbiscassi > > Linkedin - https://br.linkedin.com/in/leobiscassi > > Skype - biscassi.leo > > Twitter - https://twitter.com/leobiscassi > > > > > > ___ > > 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/ > > > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___ 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 with planemo functional tests
Hi Folks, I tried follow this tutorial [1], but I have problems in execute the command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for perform functional tests, any suggestion? Bellow some images about this problem: [image: imagem1.jpg] *Figure 1: *Command [image: imagem2.jpg] *Figure 2:* Error [image: imagem3.jpg] *Figure 3: *Galaxy Path Planemo's version is 0.23.0. [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html P.S: The command is utilized for same tool presented in tutorial. Att. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___ 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] Galaxy tools for docking protein-compounds.
Hi Bjorn, the branch model of ChemicalToolBoX is the same presented in [1]? Could guide me about it? [1] https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md Att. On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi wrote: > Ok, thanks! > > Best regards, > > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning > wrote: > >> >> >> Am 28.12.2015 um 20:33 schrieb Léo Biscassi: >> > Hi, >> > Thanks all your attention. >> > Although my project is functional prototype, its current version is >> able to >> > integrate with projects. In fact, I was looking for projects like >> > ChemicalToolBoX because I would like to develop my tools under project >> that >> > has more options. In this way, ChemicalToolBoX is a great opportunity >> for >> > me. >> > Can you update the trello card with my project? Is it necessary for your >> > organization? >> >> I added you :) So you have all right to modify cards. >> Let me know if you need help with Tool development or git. >> >> This is exciting! >> Cheers, >> Bjoern >> >> > Best regards, >> > >> > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning < >> bjoern.gruen...@gmail.com> >> > wrote: >> > >> >> >> >> >> >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi: >> >>> Hi, >> >>> >> >>> I've found this Trello card ( >> >>> https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have >> more >> >>> information about it? >> >> >> >> Afaik we can not use his work as it was done for some company and he >> >> moved on ... so this is unfortunately no option afaik. >> >> >> >> >> >> >> >>> best, >> >>> >> >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning < >> bjoern.gruen...@gmail.com >> >>> >> >>> wrote: >> >>> >> >>>> Hi, >> >>>> >> >>>> yes we had some idea, but nothing materialised so far. We started >> with >> >>>> the visualisation, because this was more fun :) >> >>>> >> >>>> Have a look at this board for more ideas: >> >>>> https://trello.com/b/t9Wr8lSY/chemicaltoolbox >> >>>> >> >>>> Ciao, >> >>>> Bjoern >> >>>> >> >>>> >> >>>> Am 28.12.2015 um 19:29 schrieb Léo Biscassi: >> >>>>> Hi Bjorn, thanks for reply. >> >>>>> Would be great idea join forces in this project. How do you plan >> extend >> >>>>> ChemicalToolBoX with docking? I would like to know more details. >> >>>>> >> >>>>> Att. >> >>>>> >> >>>>> On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning < >> >> bjoern.gruen...@gmail.com >> >>>>> >> >>>>> wrote: >> >>>>> >> >>>>>> Hi Léo, >> >>>>>> >> >>>>>> idneed we have a small community that is bringing Cheminformatics >> into >> >>>>>> the Galaxy. It's called ChemicalToolBox and is located here: >> >>>>>> >> >>>>>> >> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox >> >>>>>> >> >>>>>> We have all the basic stuff for manipulating checmical structure >> >> files, >> >>>>>> fingerprint search, pharmacophore searches and so on. Also we did >> all >> >>>>>> the basic work on datatypes and packages. Our last addition was to >> >>>>>> integrate a PDB visulalisation (NGL) based on WebGL. This one is >> used >> >> to >> >>>>>> visualise our structures directly in Galaxy. >> >>>>>> >> >>>>>> We have also a trello board with more ideas and plans what we would >> >> like >> >>>>>> to add and Vina is one of the ig targets :) >> >>>>>> Would be great if we can join forces here! >> >>>>>> >> >>>>>> We also maintain a Galaxy Flavour (Galaxy Docker Image about >> >>>>>> Cheminformatics) that we would love to extend with Docking. >> >>>>>
Re: [galaxy-dev] Happy new year!
Hi folks, happy new year! att.. On Fri, Jan 1, 2016 at 10:08 AM Sebastian Schaaf < sch...@ibe.med.uni-muenchen.de> wrote: > Hey Björn, > > Same for you, and a successful year to everyone! > Curious on your promise ;). > > Cheers, > Sebastian > > > > 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 > > ___ > > 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/ > > > -- > Sebastian Schaaf, M.Sc. Bioinformatics > Faculty Coordinator NGS Infrastructure > Chair of Biometry and Bioinformatics > Department of Medical Informatics, > Biometry and Epidemiology (IBE) > University of Munich > DKTK Munich > Marchioninistr. 15, K U1 808 > D-81377 Munich (Germany) > Tel: +49 89 4400 77499 > > ___ > 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/ -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___ 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] Galaxy tools for docking protein-compounds.
Ok, thanks! Best regards, On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning wrote: > > > Am 28.12.2015 um 20:33 schrieb Léo Biscassi: > > Hi, > > Thanks all your attention. > > Although my project is functional prototype, its current version is able > to > > integrate with projects. In fact, I was looking for projects like > > ChemicalToolBoX because I would like to develop my tools under project > that > > has more options. In this way, ChemicalToolBoX is a great opportunity for > > me. > > Can you update the trello card with my project? Is it necessary for your > > organization? > > I added you :) So you have all right to modify cards. > Let me know if you need help with Tool development or git. > > This is exciting! > Cheers, > Bjoern > > > Best regards, > > > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning > > > wrote: > > > >> > >> > >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi: > >>> Hi, > >>> > >>> I've found this Trello card ( > >>> https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have > more > >>> information about it? > >> > >> Afaik we can not use his work as it was done for some company and he > >> moved on ... so this is unfortunately no option afaik. > >> > >> > >> > >>> best, > >>> > >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning < > bjoern.gruen...@gmail.com > >>> > >>> wrote: > >>> > >>>> Hi, > >>>> > >>>> yes we had some idea, but nothing materialised so far. We started with > >>>> the visualisation, because this was more fun :) > >>>> > >>>> Have a look at this board for more ideas: > >>>> https://trello.com/b/t9Wr8lSY/chemicaltoolbox > >>>> > >>>> Ciao, > >>>> Bjoern > >>>> > >>>> > >>>> Am 28.12.2015 um 19:29 schrieb Léo Biscassi: > >>>>> Hi Bjorn, thanks for reply. > >>>>> Would be great idea join forces in this project. How do you plan > extend > >>>>> ChemicalToolBoX with docking? I would like to know more details. > >>>>> > >>>>> Att. > >>>>> > >>>>> On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning < > >> bjoern.gruen...@gmail.com > >>>>> > >>>>> wrote: > >>>>> > >>>>>> Hi Léo, > >>>>>> > >>>>>> idneed we have a small community that is bringing Cheminformatics > into > >>>>>> the Galaxy. It's called ChemicalToolBox and is located here: > >>>>>> > >>>>>> > https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox > >>>>>> > >>>>>> We have all the basic stuff for manipulating checmical structure > >> files, > >>>>>> fingerprint search, pharmacophore searches and so on. Also we did > all > >>>>>> the basic work on datatypes and packages. Our last addition was to > >>>>>> integrate a PDB visulalisation (NGL) based on WebGL. This one is > used > >> to > >>>>>> visualise our structures directly in Galaxy. > >>>>>> > >>>>>> We have also a trello board with more ideas and plans what we would > >> like > >>>>>> to add and Vina is one of the ig targets :) > >>>>>> Would be great if we can join forces here! > >>>>>> > >>>>>> We also maintain a Galaxy Flavour (Galaxy Docker Image about > >>>>>> Cheminformatics) that we would love to extend with Docking. > >>>>>> > >>>>>> Thanks for letting us know and looking forward to join forces here! > >>>>>> Bjoern > >>>>>> > >>>>>> > >>>>>> Am 28.12.2015 um 18:58 schrieb Léo Biscassi: > >>>>>>> Hi folks, > >>>>>>> > >>>>>>> I've been developing Galaxy tools for docking protein-compounds. My > >>>>>> docking > >>>>>>> program is Autodock Vina. In [1] is my repository. > >>>>>>> > >>>>>>> I'm writing here for two purpose: > >>>>>>> 1) Is there s
Re: [galaxy-dev] Galaxy tools for docking protein-compounds.
Hi, Thanks all your attention. Although my project is functional prototype, its current version is able to integrate with projects. In fact, I was looking for projects like ChemicalToolBoX because I would like to develop my tools under project that has more options. In this way, ChemicalToolBoX is a great opportunity for me. Can you update the trello card with my project? Is it necessary for your organization? Best regards, On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning wrote: > > > Am 28.12.2015 um 20:06 schrieb Léo Biscassi: > > Hi, > > > > I've found this Trello card ( > > https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have more > > information about it? > > Afaik we can not use his work as it was done for some company and he > moved on ... so this is unfortunately no option afaik. > > > > > best, > > > > On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning > > > wrote: > > > >> Hi, > >> > >> yes we had some idea, but nothing materialised so far. We started with > >> the visualisation, because this was more fun :) > >> > >> Have a look at this board for more ideas: > >> https://trello.com/b/t9Wr8lSY/chemicaltoolbox > >> > >> Ciao, > >> Bjoern > >> > >> > >> Am 28.12.2015 um 19:29 schrieb Léo Biscassi: > >>> Hi Bjorn, thanks for reply. > >>> Would be great idea join forces in this project. How do you plan extend > >>> ChemicalToolBoX with docking? I would like to know more details. > >>> > >>> Att. > >>> > >>> On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning < > bjoern.gruen...@gmail.com > >>> > >>> wrote: > >>> > >>>> Hi Léo, > >>>> > >>>> idneed we have a small community that is bringing Cheminformatics into > >>>> the Galaxy. It's called ChemicalToolBox and is located here: > >>>> > >>>> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox > >>>> > >>>> We have all the basic stuff for manipulating checmical structure > files, > >>>> fingerprint search, pharmacophore searches and so on. Also we did all > >>>> the basic work on datatypes and packages. Our last addition was to > >>>> integrate a PDB visulalisation (NGL) based on WebGL. This one is used > to > >>>> visualise our structures directly in Galaxy. > >>>> > >>>> We have also a trello board with more ideas and plans what we would > like > >>>> to add and Vina is one of the ig targets :) > >>>> Would be great if we can join forces here! > >>>> > >>>> We also maintain a Galaxy Flavour (Galaxy Docker Image about > >>>> Cheminformatics) that we would love to extend with Docking. > >>>> > >>>> Thanks for letting us know and looking forward to join forces here! > >>>> Bjoern > >>>> > >>>> > >>>> Am 28.12.2015 um 18:58 schrieb Léo Biscassi: > >>>>> Hi folks, > >>>>> > >>>>> I've been developing Galaxy tools for docking protein-compounds. My > >>>> docking > >>>>> program is Autodock Vina. In [1] is my repository. > >>>>> > >>>>> I'm writing here for two purpose: > >>>>> 1) Is there someone working in this way? I've found the project [2]. > >>>>> 2) I would like to share these tools to Galaxy project. Are they > >> welcome > >>>>> for Galaxy project? Let me know the best practices for developing > >> tools > >>>> to > >>>>> be shared in Galaxy project. > >>>>> > >>>>> [1] https://github.com/leobiscassi/galaxy_tools > >>>>> [2] https://toolshed.g2.bx.psu.edu/ > >>>>> > >>>>> Thanks for any help. > >>>>> > >>>>> Att. > >>>>> > >>>>> > >>>>> > >>>>> ___ > >>>>> 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/ > >>>>> > >>>> > >> > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___ 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] Galaxy tools for docking protein-compounds.
Hi, I've found this Trello card ( https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have more information about it? best, On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning wrote: > Hi, > > yes we had some idea, but nothing materialised so far. We started with > the visualisation, because this was more fun :) > > Have a look at this board for more ideas: > https://trello.com/b/t9Wr8lSY/chemicaltoolbox > > Ciao, > Bjoern > > > Am 28.12.2015 um 19:29 schrieb Léo Biscassi: > > Hi Bjorn, thanks for reply. > > Would be great idea join forces in this project. How do you plan extend > > ChemicalToolBoX with docking? I would like to know more details. > > > > Att. > > > > On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning > > > wrote: > > > >> Hi Léo, > >> > >> idneed we have a small community that is bringing Cheminformatics into > >> the Galaxy. It's called ChemicalToolBox and is located here: > >> > >> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox > >> > >> We have all the basic stuff for manipulating checmical structure files, > >> fingerprint search, pharmacophore searches and so on. Also we did all > >> the basic work on datatypes and packages. Our last addition was to > >> integrate a PDB visulalisation (NGL) based on WebGL. This one is used to > >> visualise our structures directly in Galaxy. > >> > >> We have also a trello board with more ideas and plans what we would like > >> to add and Vina is one of the ig targets :) > >> Would be great if we can join forces here! > >> > >> We also maintain a Galaxy Flavour (Galaxy Docker Image about > >> Cheminformatics) that we would love to extend with Docking. > >> > >> Thanks for letting us know and looking forward to join forces here! > >> Bjoern > >> > >> > >> Am 28.12.2015 um 18:58 schrieb Léo Biscassi: > >>> Hi folks, > >>> > >>> I've been developing Galaxy tools for docking protein-compounds. My > >> docking > >>> program is Autodock Vina. In [1] is my repository. > >>> > >>> I'm writing here for two purpose: > >>> 1) Is there someone working in this way? I've found the project [2]. > >>> 2) I would like to share these tools to Galaxy project. Are they > welcome > >>> for Galaxy project? Let me know the best practices for developing > tools > >> to > >>> be shared in Galaxy project. > >>> > >>> [1] https://github.com/leobiscassi/galaxy_tools > >>> [2] https://toolshed.g2.bx.psu.edu/ > >>> > >>> Thanks for any help. > >>> > >>> Att. > >>> > >>> > >>> > >>> ___ > >>> 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/ > >>> > >> > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___ 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] Galaxy tools for docking protein-compounds.
Hi Martin, I'll take a look at the tutorials, thanks! Att. On Mon, Dec 28, 2015 at 4:10 PM Martin Čech wrote: > Hello Léo, > > all tool are sincerely welcomed in the Galaxy Tool Shed. > > Good tutorial for tool writing is a part of Planemo documentation: > https://planemo.readthedocs.org/en/latest/writing.html > Planemo is a command line toolset aimed at helping tool developers like > you getting their tools into Galaxy and the Tool Shed. > Also have a look at https://github.com/galaxyproject/tools-iuc for tool > writing inspiration and > http://galaxy-iuc-standards.readthedocs.org/en/latest/ for best practices. > > Let us know if we can help. > > Thank you for using Galaxy. > > M. > > On Mon, Dec 28, 2015 at 12:58 PM Léo Biscassi > wrote: > >> Hi folks, >> >> I've been developing Galaxy tools for docking protein-compounds. My >> docking program is Autodock Vina. In [1] is my repository. >> >> I'm writing here for two purpose: >> 1) Is there someone working in this way? I've found the project [2]. >> 2) I would like to share these tools to Galaxy project. Are they welcome >> for Galaxy project? Let me know the best practices for developing tools to >> be shared in Galaxy project. >> >> [1] https://github.com/leobiscassi/galaxy_tools >> [2] https://toolshed.g2.bx.psu.edu/ >> >> Thanks for any help. >> >> Att. >> -- >> *Léo Biscassi* >> Facebook - https://pt-br.facebook.com/lbiscassi >> Linkedin - https://br.linkedin.com/in/leobiscassi >> Skype - biscassi.leo >> Twitter - https://twitter.com/leobiscassi >> > ___ >> 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/ > > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___ 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] Galaxy tools for docking protein-compounds.
Hi Bjorn, thanks for reply. Would be great idea join forces in this project. How do you plan extend ChemicalToolBoX with docking? I would like to know more details. Att. On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning wrote: > Hi Léo, > > idneed we have a small community that is bringing Cheminformatics into > the Galaxy. It's called ChemicalToolBox and is located here: > > https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox > > We have all the basic stuff for manipulating checmical structure files, > fingerprint search, pharmacophore searches and so on. Also we did all > the basic work on datatypes and packages. Our last addition was to > integrate a PDB visulalisation (NGL) based on WebGL. This one is used to > visualise our structures directly in Galaxy. > > We have also a trello board with more ideas and plans what we would like > to add and Vina is one of the ig targets :) > Would be great if we can join forces here! > > We also maintain a Galaxy Flavour (Galaxy Docker Image about > Cheminformatics) that we would love to extend with Docking. > > Thanks for letting us know and looking forward to join forces here! > Bjoern > > > Am 28.12.2015 um 18:58 schrieb Léo Biscassi: > > Hi folks, > > > > I've been developing Galaxy tools for docking protein-compounds. My > docking > > program is Autodock Vina. In [1] is my repository. > > > > I'm writing here for two purpose: > > 1) Is there someone working in this way? I've found the project [2]. > > 2) I would like to share these tools to Galaxy project. Are they welcome > > for Galaxy project? Let me know the best practices for developing tools > to > > be shared in Galaxy project. > > > > [1] https://github.com/leobiscassi/galaxy_tools > > [2] https://toolshed.g2.bx.psu.edu/ > > > > Thanks for any help. > > > > Att. > > > > > > > > ___ > > 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/ > > > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___ 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] Galaxy tools for docking protein-compounds.
Hi folks, I've been developing Galaxy tools for docking protein-compounds. My docking program is Autodock Vina. In [1] is my repository. I'm writing here for two purpose: 1) Is there someone working in this way? I've found the project [2]. 2) I would like to share these tools to Galaxy project. Are they welcome for Galaxy project? Let me know the best practices for developing tools to be shared in Galaxy project. [1] https://github.com/leobiscassi/galaxy_tools [2] https://toolshed.g2.bx.psu.edu/ Thanks for any help. Att. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___ 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] Tool with multiple outputs.
Hi Bjoern, I'll try to use collections and return soon. I could not find the tag of the documentation [1], has any record in the documentation about it? [1] https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Thanks for the reply. Att. On Fri, Sep 11, 2015 at 5:42 AM, Bjoern Gruening wrote: > Hi Léo, > > maybe you can use a dataset collection instead. This is a new way to > handle multiple datasets of the same type. > > For an example see this tool: > > https://github.com/bgruening/galaxytools/blob/master/tools/rna_tools/rna_shapes/RNAShapes.xml#L218 > > Cheers, > Bjoern > > On 10.09.2015 23:01, Léo Biscassi wrote: > > Good afternoon people! > I am developing a tool that will have multiple outputs where they have to > be data sets in history. > Read the tutorial [1] and from it developed my [2] [3] tool, however, have > only the .txt output file, the .mol2 files are not showing up in history, > someone can tell me why? > > [1] > https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Handling_Multiple_Output_Files_in_Galaxy > [2] https://gist.github.com/leobiscassi/8058b6307d388167866a > [3] https://gist.github.com/leobiscassi/bc54a7df261c4ee81aa9 > > Att. > -- > *Léo Biscassi* > Facebook - https://pt-br.facebook.com/lbiscassi > Linkedin - https://br.linkedin.com/in/leobiscassi > Skype - biscassi.leo > Twitter - https://twitter.com/leobiscassi > >- > > > > > ___ > 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/ > > > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi - ___ 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] Tool with multiple outputs.
Hi Christian, Yes, I remembered to refresh tool panel. Thanks for the reply. Att. On Fri, Sep 11, 2015 at 5:02 AM, Christian Brenninkmeijer < christian.brenninkmei...@manchester.ac.uk> wrote: > Hi, > Did you remember to refresh the history panel after the tool finished? > That caught me out multiple times when testing multiple outputs. > > Christian > -- > *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf > of Léo Biscassi [leo.bisca...@gmail.com] > *Sent:* Thursday, September 10, 2015 10:01 PM > *To:* galaxy-dev@lists.galaxyproject.org > *Subject:* [galaxy-dev] Tool with multiple outputs. > > Good afternoon people! > I am developing a tool that will have multiple outputs where they have to > be data sets in history. > Read the tutorial [1] and from it developed my [2] [3] tool, however, have > only the .txt output file, the .mol2 files are not showing up in history, > someone can tell me why? > > [1] > https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Handling_Multiple_Output_Files_in_Galaxy > [2] https://gist.github.com/leobiscassi/8058b6307d388167866a > [3] https://gist.github.com/leobiscassi/bc54a7df261c4ee81aa9 > > Att. > -- > *Léo Biscassi* > Facebook - https://pt-br.facebook.com/lbiscassi > Linkedin - https://br.linkedin.com/in/leobiscassi > Skype - biscassi.leo > Twitter - https://twitter.com/leobiscassi > >- > > > -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi - ___ 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] Tool with multiple outputs.
Good afternoon people! I am developing a tool that will have multiple outputs where they have to be data sets in history. Read the tutorial [1] and from it developed my [2] [3] tool, however, have only the .txt output file, the .mol2 files are not showing up in history, someone can tell me why? [1] https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Handling_Multiple_Output_Files_in_Galaxy [2] https://gist.github.com/leobiscassi/8058b6307d388167866a [3] https://gist.github.com/leobiscassi/bc54a7df261c4ee81aa9 Att. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi - ___ 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] Problem with ChemicalToolBox dependencies
Hello everyone! I have a Problem when installing the tool ChemicalToolBox. The error occurs in eigen3 dependence: CMake Error: The following variables are used in this project, but They are set to NOTFOUND. PLEASE SET Them or make sure They are set and tested Correctly in the CMake files: GLUT_Xi_LIBRARY (ADVANCED) linked by target "openglsupport" in directory /home/leobiscassi/programs/galaxy/database/tmp/tmp-toolshed-mtdvbBrUS/eigen-eigen-2249f9c22fe8/unsupported/test GLUT_Xmu_LIBRARY (ADVANCED) linked by target "openglsupport" in directory /home/leobiscassi/programs/galaxy/database/tmp/tmp-toolshed-mtdvbBrUS/eigen-eigen-2249f9c22fe8/unsupported/test I'm with the prerequisites installed: * Python 2.6 or 2.7 * Standard C compiler, C ++ and Fortran compiler * Autotools * CMake * Cairo development files (used for PNG depictions) * Python development files * Libblas and liblapack development files * Java Runtime Environment (JRE, used by opsin and NPLs) And the packages installed according to the instructions on github [1]: Debian based systems: apt-get install build-essential cmake gfortran mercurial libcairo2-dev python-dev And the OpenGL package: apt-get install freeglut3-dev [1] https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox Has anyone had a similar experience? I am using ubuntu 14.04 Att. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi - ___ 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/
