[galaxy-dev] Re: pbs_python + python 3 issue
From the syntax I can see pbs-python still uses a Python 2 style print, it will need updating for Python 3. I suggest opening an issue on the repository, and seeing what the author says. I would guess the Python 2 to 3 changes will be fairly easy, but worry that there have been other changes to Galaxy in the meantime which would be more trouble for this PBS extension as it does not appear to have been updated for 6 years. Peter On Mon, Nov 9, 2020 at 5:34 AM Sandra Maksimovic wrote: > > Hi, > > Has anyone out there had any success installing the pbs_python module into a > Python 3+ Galaxy installation? I run into the following issue when installing > https://github.com/ehiggs/pbs-python as per the documentation. > > # python setup.py install > File "setup.py", line 68 > print "Version: %s is not supported" %(PBS_VERSION) >^ > SyntaxError: invalid syntax > > I provide the PBS/Torque version via the PBS_PYTHON_INCLUDE_DIR environment > variable but it doesn't seem to detect the version properly. > > Thanks, > Sandra > > Disclaimer > > This e-mail and any attachments to it (the "Communication") are, unless > otherwise stated, confidential, may contain copyright material and is for the > use only of the intended recipient. If you receive the Communication in > error, please notify the sender immediately by return e-mail, delete the > Communication and the return e-mail, and do not read, copy, retransmit or > otherwise deal with it. Any views expressed in the Communication are those of > the individual sender only, unless expressly stated to be those of Murdoch > Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related > entities. MCRI does not accept liability in connection with the integrity of > or errors in the Communication, computer virus, data corruption, interference > or delay arising from or in respect of the Communication. > ___ > 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: > %(web_page_url)s > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: How to include a large datafile in a bioconda package?
That seems a good compromise within conda, since BioConda wouldn't want the binary package itself to be too big. (I'm doing something similar with some real sample data for a tool, putting it up on Zenodo. Of course, this is optional for my tool - your use case is different.) The Galaxy Data Manager route seems more appropriate if there is a choice of large data files which could be used with the tool (not just one). Peter On Wed, Jul 24, 2019 at 10:26 PM Björn Grüning wrote: > > Hi Jin, > > you can use a post-link script in conda. > > Like here: > https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picrust2/post-link.sh > > This way the data can be fetch during tool installation. > > See more information here: > https://docs.conda.io/projects/conda-build/en/latest/resources/link-scripts.html > > Ciao, > Bjoern > > Am 24.07.19 um 18:43 schrieb Jin Li: > > Hi Brad, > > > > Thank you for your quick reply. I can put the data file to Zenodo so > > that I will have a permanent location for it. > > > > As for re-computing the data file locally, it may need several days to > > run, so it may be quite inefficient to do the computing. I am > > expecting an automatic download of the data file when installing the > > package. Do we have a convention to do that? Thank you. > > > > Best regards, > > Jin > > > > On Wed, Jul 24, 2019 at 11:31 AM Langhorst, Brad wrote: > >> > >> Hi: > >> > >> I’d be concerned about that file changing or disappearing and causing > >> irreproducibility. > >> If the URL were to a permanent location (e.g. NCBI or zenodo) maybe it’s > >> ok. > >> > >> Could it be re-computed locally if necessary (like a genome index)? > >> > >> Maybe others know of examples where this is done. > >> > >> > >> Brad > >> > >> On Jul 24, 2019, at 12:24 PM, Jin Li wrote: > >> > >> Hi all, > >> > >> I am not sure if this mailing list is a good place to ask a bioconda > >> question. Sorry to bother if not. I want to ask how to include a large > >> data file when publishing a bioconda package. Our program depends on a > >> pre-computed data file, which is too large to be included in the > >> source code package. The data file can be accessed via a public URL. > >> Can I put the downloading command in `build.sh` when publishing a > >> bioconda package? If not, do we have a convention to deal with > >> dependent large datafiles? Thank you. > >> > >> Best regards, > >> Jin > >> ___ > >> 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: > >> %(web_page_url)s > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/ > >> > >> > >> Bradley W. Langhorst, Ph.D. > >> Development Group Leader > >> New England Biolabs > >> > >> > >> > > ___ > > 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: > >%(web_page_url)s > > > > To search Galaxy mailing lists use the unified search at: > >http://galaxyproject.org/search/ > > > ___ > 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: > %(web_page_url)s > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: Share Docker Volumes when integrating Containers in Galaxy
I don't have any advise from the BLAST DB side, but I would expect the same solution to work with any *.loc file and the file system it points at. Peter On Mon, May 20, 2019 at 10:50 AM Schäfer, Richard wrote: > > Hello, > > I want to integrate a Docker container as a tool in Galaxy. This works great. > However, > I need the forward a Volume to the container (at least that how it works > outside of Galaxy). > In particular, this would be the BLAST database. > > This means, I would want to share the location specified in blastdb.loc and > forward it to the > container. Is there a way to do this? > > I see that there is an option to expose volumes to containers by specifying > it in the job.conf.xml > > id="docker_volumes">$defaults,/mnt/galaxyData/libraries:ro,/mnt/galaxyData/indices:ro > > However, I guess this will then be done for all containers? And how do I > integrate blastdb.loc in that command? > For that, my tool config looks like this: > > > > > > > > > I simply want to access the path inside of the container and therefore shared > it with the container. > > Thanks for any help > > Cheers > Rich > ___ > 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: > %(web_page_url)s > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ 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: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
