Hello all, How do tool wrapper developers/packagers go about adding entries to the Galaxy depot? There isn't a GitHub repository for this is there? Specifically I want to upload some older MIRA releases, e.g. these URLs have broken, but I have the original files and checksums: http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mir... http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mir... See also: https://www.freelists.org/post/mira_talk/Stable-download-URLs-on-sourceforge https://www.freelists.org/post/mira_talk/MIRA-495-now-missing-on-SourceForge I'm now running "planemo lint --urls ..." under TravisCI which flags the broken URLs immediately (rather than finding out when the installation fails later): https://github.com/peterjc/galaxy_mira/commit/4e26a4e3f3d69adaab657cb614e56e... https://travis-ci.org/peterjc/galaxy_mira/jobs/150025836 Regards, Peter
Hi Peter, The cargo port is the ideal place for this, however it does not support manual uploads of files. On 08. aug. 2016 13:37, Peter Cock wrote:
Hello all,
How do tool wrapper developers/packagers go about adding entries to the Galaxy depot? There isn't a GitHub repository for this is there?
Specifically I want to upload some older MIRA releases, e.g. these URLs have broken, but I have the original files and checksums:
http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mir... http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mir... I would recommend the following though others who work on the cargo port might chime in:
* Upload those tarballs somewhere accessible * Add cargo port entries with your URLs Then cargo port would at least have a copy you can reference in your tools.
See also:
https://www.freelists.org/post/mira_talk/Stable-download-URLs-on-sourceforge https://www.freelists.org/post/mira_talk/MIRA-495-now-missing-on-SourceForge
I'm now running "planemo lint --urls ..." under TravisCI which flags the broken URLs immediately (rather than finding out when the installation fails later):
https://github.com/peterjc/galaxy_mira/commit/4e26a4e3f3d69adaab657cb614e56e... https://travis-ci.org/peterjc/galaxy_mira/jobs/150025836
Regards,
Peter ___________________________________________________________ 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/
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-- Eric Rasche Programmer II Center for Phage Technology Rm 312A, Biochemistry & Biophysics Texas A&M University College Station, TX 77843 esr@tamu.edu <mailto:esr@tamu.edu>
On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <esr@tamu.edu> wrote:
Hi Peter,
The cargo port is the ideal place for this, however it does not support manual uploads of files.
Thanks Eric, You mean https://github.com/galaxyproject/cargo-port Is that something which might be addressed in future? The use case is when a previously public file stops working (either temporarily or permanently), so you can't use the official URL to make the cached copy? Would it be OK to use a short lived URL like a personal dropbox URL, and then once cached, update urls.tsv with the original official (but broken) URL? Peter
Hi Peter, Am 08.08.2016 um 15:54 schrieb Peter Cock:
On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <esr@tamu.edu> wrote:
Hi Peter,
The cargo port is the ideal place for this, however it does not support manual uploads of files.
Thanks Eric,
You mean https://github.com/galaxyproject/cargo-port
Is that something which might be addressed in future? The use case is when a previously public file stops working (either temporarily or permanently), so you can't use the official URL to make the cached copy?
Would it be OK to use a short lived URL like a personal dropbox URL, and then once cached, update urls.tsv with the original official (but broken) URL?
Yes this is totally fine. We just need to have a way to verify and check tarballs before upload and we thought github and PR are a nice fit for this. Thanks, Bjoern
Peter ___________________________________________________________ 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/
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On Mon, Aug 8, 2016 at 3:27 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Peter,
Am 08.08.2016 um 15:54 schrieb Peter Cock:
On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <esr@tamu.edu> wrote:
Hi Peter,
The cargo port is the ideal place for this, however it does not support manual uploads of files.
Thanks Eric,
You mean https://github.com/galaxyproject/cargo-port
Is that something which might be addressed in future? The use case is when a previously public file stops working (either temporarily or permanently), so you can't use the official URL to make the cached copy?
Would it be OK to use a short lived URL like a personal dropbox URL, and then once cached, update urls.tsv with the original official (but broken) URL?
Yes this is totally fine. We just need to have a way to verify and check tarballs before upload and we thought github and PR are a nice fit for this.
Thanks, Bjoern
Let's try this then: https://github.com/galaxyproject/cargo-port/pull/82 (I can't find the Mac binaries for MIRA 4.9.5, hopefully I might have that on my home machine but it's a long shot.) Peter
Peter: depot is something we plan on maintaining and providing as a service as long as Galaxy. The cargo-port we will also expand in future (eg to provide dynamic fallback at installation time. It is the right place to put your mira backups (and any other packages you care about in recipes). Cheers, M. On Mon, Aug 8, 2016 at 9:54 AM Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <esr@tamu.edu> wrote:
Hi Peter,
The cargo port is the ideal place for this, however it does not support manual uploads of files.
Thanks Eric,
You mean https://github.com/galaxyproject/cargo-port
Is that something which might be addressed in future? The use case is when a previously public file stops working (either temporarily or permanently), so you can't use the official URL to make the cached copy?
Would it be OK to use a short lived URL like a personal dropbox URL, and then once cached, update urls.tsv with the original official (but broken) URL?
Peter ___________________________________________________________ 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/
participants (4)
-
Björn Grüning -
Eric Rasche -
Martin Čech -
Peter Cock