Re: [galaxy-dev] Importing workflows via command-line/Docker script
Sure, if you are fast we can include this in the galaxy-stable:16.01 release which will be release very soon. You can also create a PR against the 16.01 branch on: https://github.com/bgruening/docker-galaxy-stable/tree/16.01 Ciao, Bjoern Am 27.01.2016 um 09:22 schrieb Cameron Jack: > Thanks for the quick response Marius and Bjoern, really appreciate the > help! > > Since I need to make this work in the next day or so, would you be > interested in seeing what my script looks like Bjoern? I imagine it¹ll > only be a couple of lines though to do this. > > Thanks again, > Cam > > On 27/01/2016 7:17 pm, "Björn Grüning" wrote: > >> Hi Cam, >> >> as Marius already pointed out this is easily possible with bioblend. >> I would create a small script that takes the path to the GA file as >> input, preferably also a URL, and populates this in Galaxy. >> >> I would be interested to include such a script in the Main Docker >> container, so everyone can use this similar to the script for installing >> tools. >> >> A second option would be to upload the workflow with all dependencies to >> the TS and than simply install the workflow. >> >> Similar to this one: >> >> https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_ >> plus/find_three_genes_located_nearby >> >> Hope this helps, >> Bjoern >> >> Am 27.01.2016 um 03:14 schrieb Cameron Jack: >>> Hi all, >>> >>> >>> I've been developing a Dockerfile and repositories to enable users to >>> set up an NGS forensics pipeline. So far so good, I can build the image >>> (based on Bjoern Gruening's excellent galaxy-stable Docker image) and >>> incorporate all the various tools I need, including custom ones with >>> custom interfaces. I've also built some workflows within a running image >>> and exported them to .ga files, but now I'm wondering if there is a way >>> to import those back in to a new image via the Dockerfile? I'd rather >>> have everything set up for the users upon building the image, rather >>> than logging in as admin and then importing the workflow. Is this >>> possible? If so, how? >>> >>> >>> Thanks for any and all answers. >>> >>> >>> Best regards, >>> >>> Cam >>> >>> >>> Cameron Jack >>> >>> Bioinformatician >>> ANU Bioinformatics Consulting Unit >>> The Australian National University >>> >>> The John Curtin School of Medical Research >>> Building 131 Garran Road >>> Acton 0200, ACT >>> >>> Ph (office): +61 2 612 51128 >>> Ph (mobile): +61 4 2368 0745 >>> Email: cameron.j...@anu.edu.au >>> Group email: a...@anu.edu.au >>> >>> >>> ___ >>> 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/ >>> > > ___ > 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/ > ___ 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] Importing workflows via command-line/Docker script
Thanks for the quick response Marius and Bjoern, really appreciate the help! Since I need to make this work in the next day or so, would you be interested in seeing what my script looks like Bjoern? I imagine it¹ll only be a couple of lines though to do this. Thanks again, Cam On 27/01/2016 7:17 pm, "Björn Grüning" wrote: >Hi Cam, > >as Marius already pointed out this is easily possible with bioblend. >I would create a small script that takes the path to the GA file as >input, preferably also a URL, and populates this in Galaxy. > >I would be interested to include such a script in the Main Docker >container, so everyone can use this similar to the script for installing >tools. > >A second option would be to upload the workflow with all dependencies to >the TS and than simply install the workflow. > >Similar to this one: > >https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_ >plus/find_three_genes_located_nearby > >Hope this helps, >Bjoern > >Am 27.01.2016 um 03:14 schrieb Cameron Jack: >> Hi all, >> >> >> I've been developing a Dockerfile and repositories to enable users to >> set up an NGS forensics pipeline. So far so good, I can build the image >> (based on Bjoern Gruening's excellent galaxy-stable Docker image) and >> incorporate all the various tools I need, including custom ones with >> custom interfaces. I've also built some workflows within a running image >> and exported them to .ga files, but now I'm wondering if there is a way >> to import those back in to a new image via the Dockerfile? I'd rather >> have everything set up for the users upon building the image, rather >> than logging in as admin and then importing the workflow. Is this >> possible? If so, how? >> >> >> Thanks for any and all answers. >> >> >> Best regards, >> >> Cam >> >> >> Cameron Jack >> >> Bioinformatician >> ANU Bioinformatics Consulting Unit >> The Australian National University >> >> The John Curtin School of Medical Research >> Building 131 Garran Road >> Acton 0200, ACT >> >> Ph (office): +61 2 612 51128 >> Ph (mobile): +61 4 2368 0745 >> Email: cameron.j...@anu.edu.au >> Group email: a...@anu.edu.au >> >> >> ___ >> 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/ >> ___ 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] Importing workflows via command-line/Docker script
Hi Cam, as Marius already pointed out this is easily possible with bioblend. I would create a small script that takes the path to the GA file as input, preferably also a URL, and populates this in Galaxy. I would be interested to include such a script in the Main Docker container, so everyone can use this similar to the script for installing tools. A second option would be to upload the workflow with all dependencies to the TS and than simply install the workflow. Similar to this one: https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby Hope this helps, Bjoern Am 27.01.2016 um 03:14 schrieb Cameron Jack: > Hi all, > > > I've been developing a Dockerfile and repositories to enable users to > set up an NGS forensics pipeline. So far so good, I can build the image > (based on Bjoern Gruening's excellent galaxy-stable Docker image) and > incorporate all the various tools I need, including custom ones with > custom interfaces. I've also built some workflows within a running image > and exported them to .ga files, but now I'm wondering if there is a way > to import those back in to a new image via the Dockerfile? I'd rather > have everything set up for the users upon building the image, rather > than logging in as admin and then importing the workflow. Is this > possible? If so, how? > > > Thanks for any and all answers. > > > Best regards, > > Cam > > > Cameron Jack > > Bioinformatician > ANU Bioinformatics Consulting Unit > The Australian National University > > The John Curtin School of Medical Research > Building 131 Garran Road > Acton 0200, ACT > > Ph (office): +61 2 612 51128 > Ph (mobile): +61 4 2368 0745 > Email: cameron.j...@anu.edu.au > Group email: a...@anu.edu.au > > > ___ > 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/ > ___ 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] Importing workflows via command-line/Docker script
Hi Cam, this would be possible using bioblend ( https://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html?highlight=workflow#module-bioblend.galaxy.workflows). Take a look at the `import_workflow_from_local_path` function. You'll need to have galaxy running for this (same as for installing tools). Cheers, Marius On 27 January 2016 at 03:14, Cameron Jack wrote: > Hi all, > > > I've been developing a Dockerfile and repositories to enable users to set > up an NGS forensics pipeline. So far so good, I can build the image (based > on Bjoern Gruening's excellent galaxy-stable Docker image) and incorporate > all the various tools I need, including custom ones with custom interfaces. > I've also built some workflows within a running image and exported them to > .ga files, but now I'm wondering if there is a way to import those back in > to a new image via the Dockerfile? I'd rather have everything set up for > the users upon building the image, rather than logging in as admin and then > importing the workflow. Is this possible? If so, how? > > > Thanks for any and all answers. > > > Best regards, > > Cam > > > Cameron Jack > > Bioinformatician > ANU Bioinformatics Consulting Unit > The Australian National University > > The John Curtin School of Medical Research > Building 131 Garran Road > Acton 0200, ACT > > Ph (office): +61 2 612 51128 > Ph (mobile): +61 4 2368 0745 > Email: cameron.j...@anu.edu.au > Group email: a...@anu.edu.au > > ___ > 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/ > ___ 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/
