From pvh@sanbi.ac.za Fri Mar 18 15:16:43 2016 From: Peter van Heusden To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo update failing on testtoolshed Date: Fri, 18 Mar 2016 21:16:42 +0200 Message-ID: In-Reply-To: <56EC52FE.5000404@gmail.com> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============8445173521020501086==" --===============8445173521020501086== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable The repo is empty, so there is nothing to delete at this stage. And I can't figure out how to delete the thing entirely. I looked at the splitFasta tool, and also the splitfasta tool from rnateam (in the test toolshed) and these split into 1 file for each sequence as opposed to a certain number of chunks. Peter On 18 March 2016 at 21:11, Bj=C3=B6rn Gr=C3=BCning wrote: > Hi Peter, > > can you try to delete files with the web interface? > > I saw the tool name, do you know this small tool? > > https://github.com/bgruening/galaxytools/blob/master/tools/splitfasta/split= Fasta.xml > > Cheers, > Bjoern > > Am 18.03.2016 um 20:03 schrieb Peter van Heusden: > > Hi there > > > > I'm trying to update a newly created tool on the test tool shed and I > > get this error: > > > > $ planemo shed_update -t testtoolshed > > cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git rev-parse HEAD > > cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git diff --quiet > > Could not update split_fasta_chunks > > Unexpected response from galaxy: 500: > > Internal Server Error > > > >

Internal Server Error

> >

The server has either erred or is incapable of performing > > the requested operation. > > > >
> >

> >

WSGI Server

> > > > > > > > Repository metadata updated. > > Failed to update a repository. > > > > I might have accidentally created a "bad" repository that is leading to > > this error. This is with version 0.23.0. Alternately, is there a way to > > delete the tool so that I can try and recreate it? > > > > Thanks! > > 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/ > > > --===============8445173521020501086== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGRpdiBkaXI9Imx0ciI+VGhlIHJlcG8gaXMgZW1wdHksIHNvIHRoZXJlIGlzIG5vdGhpbmcgdG8g ZGVsZXRlIGF0IHRoaXMgc3RhZ2UuIEFuZCBJIGNhbiYjMzk7dCBmaWd1cmUgb3V0IGhvdyB0byBk ZWxldGUgdGhlIHRoaW5nIGVudGlyZWx5LjxkaXY+PGJyPjwvZGl2PjxkaXY+SSBsb29rZWQgYXQg dGhlIHNwbGl0RmFzdGEgdG9vbCwgYW5kIGFsc28gdGhlIHNwbGl0ZmFzdGEgdG9vbCBmcm9tIHJu YXRlYW0gKGluIHRoZSB0ZXN0IHRvb2xzaGVkKSBhbmQgdGhlc2Ugc3BsaXQgaW50byAxIGZpbGUg Zm9yIGVhY2ggc2VxdWVuY2UgYXMgb3Bwb3NlZCB0byBhIGNlcnRhaW4gbnVtYmVyIG9mIGNodW5r cy48L2Rpdj48ZGl2Pjxicj48L2Rpdj48ZGl2PlBldGVyPC9kaXY+PC9kaXY+PGRpdiBjbGFzcz0i Z21haWxfZXh0cmEiPjxicj48ZGl2IGNsYXNzPSJnbWFpbF9xdW90ZSI+T24gMTggTWFyY2ggMjAx NiBhdCAyMToxMSwgQmrDtnJuIEdyw7xuaW5nIDxzcGFuIGRpcj0ibHRyIj4mbHQ7PGEgaHJlZj0i bWFpbHRvOmJqb2Vybi5ncnVlbmluZ0BnbWFpbC5jb20iIHRhcmdldD0iX2JsYW5rIj5iam9lcm4u Z3J1ZW5pbmdAZ21haWwuY29tPC9hPiZndDs8L3NwYW4+IHdyb3RlOjxicj48YmxvY2txdW90ZSBj bGFzcz0iZ21haWxfcXVvdGUiIHN0eWxlPSJtYXJnaW46MCAwIDAgLjhleDtib3JkZXItbGVmdDox cHggI2NjYyBzb2xpZDtwYWRkaW5nLWxlZnQ6MWV4Ij5IaSBQZXRlciw8YnI+Cjxicj4KY2FuIHlv dSB0cnkgdG8gZGVsZXRlIGZpbGVzIHdpdGggdGhlIHdlYiBpbnRlcmZhY2U/PGJyPgo8YnI+Ckkg c2F3IHRoZSB0b29sIG5hbWUsIGRvIHlvdSBrbm93IHRoaXMgc21hbGwgdG9vbD88YnI+CjxhIGhy ZWY9Imh0dHBzOi8vZ2l0aHViLmNvbS9iZ3J1ZW5pbmcvZ2FsYXh5dG9vbHMvYmxvYi9tYXN0ZXIv dG9vbHMvc3BsaXRmYXN0YS9zcGxpdEZhc3RhLnhtbCIgcmVsPSJub3JlZmVycmVyIiB0YXJnZXQ9 Il9ibGFuayI+aHR0cHM6Ly9naXRodWIuY29tL2JncnVlbmluZy9nYWxheHl0b29scy9ibG9iL21h c3Rlci90b29scy9zcGxpdGZhc3RhL3NwbGl0RmFzdGEueG1sPC9hPjxicj4KPGJyPgpDaGVlcnMs PGJyPgpCam9lcm48YnI+CjxkaXY+PGRpdiBjbGFzcz0iaDUiPjxicj4KQW0gMTguMDMuMjAxNiB1 bSAyMDowMyBzY2hyaWViIFBldGVyIHZhbiBIZXVzZGVuOjxicj4KJmd0OyBIaSB0aGVyZTxicj4K Jmd0Ozxicj4KJmd0OyBJJiMzOTttIHRyeWluZyB0byB1cGRhdGUgYSBuZXdseSBjcmVhdGVkIHRv b2wgb24gdGhlIHRlc3QgdG9vbCBzaGVkIGFuZCBJPGJyPgomZ3Q7IGdldCB0aGlzIGVycm9yOjxi cj4KJmd0Ozxicj4KJmd0OyAkIHBsYW5lbW8gc2hlZF91cGRhdGUgLXQgdGVzdHRvb2xzaGVkPGJy PgomZ3Q7IGNkICYjMzk7L2hvbWUvcHZoL1B5Y2hhcm1Qcm9qZWN0cy9zcGxpdF9mYXN0YV9jaHVu a3MmIzM5OyAmYW1wOyZhbXA7IGdpdCByZXYtcGFyc2UgSEVBRDxicj4KJmd0OyBjZCAmIzM5Oy9o b21lL3B2aC9QeWNoYXJtUHJvamVjdHMvc3BsaXRfZmFzdGFfY2h1bmtzJiMzOTsgJmFtcDsmYW1w OyBnaXQgZGlmZiAtLXF1aWV0PGJyPgomZ3Q7IENvdWxkIG5vdCB1cGRhdGUgc3BsaXRfZmFzdGFf Y2h1bmtzPGJyPgomZ3Q7IFVuZXhwZWN0ZWQgcmVzcG9uc2UgZnJvbSBnYWxheHk6IDUwMDogJmx0 O2h0bWwmZ3Q7PGJyPgomZ3Q7wqAgwqAmbHQ7aGVhZCZndDsmbHQ7dGl0bGUmZ3Q7SW50ZXJuYWwg U2VydmVyIEVycm9yJmx0Oy90aXRsZSZndDsmbHQ7L2hlYWQmZ3Q7PGJyPgomZ3Q7wqAgwqAmbHQ7 Ym9keSZndDs8YnI+CiZndDvCoCDCoCDCoCZsdDtoMSZndDtJbnRlcm5hbCBTZXJ2ZXIgRXJyb3Im bHQ7L2gxJmd0Ozxicj4KJmd0O8KgIMKgIMKgJmx0O3AmZ3Q7VGhlIHNlcnZlciBoYXMgZWl0aGVy IGVycmVkIG9yIGlzIGluY2FwYWJsZSBvZiBwZXJmb3JtaW5nPGJyPgomZ3Q7IHRoZSByZXF1ZXN0 ZWQgb3BlcmF0aW9uLjxicj4KJmd0Ozxicj4KJmd0OyAmbHQ7YnIvJmd0Ozxicj4KJmd0OyAmbHQ7 IS0twqAgLS0mZ3Q7Jmx0Oy9wJmd0Ozxicj4KJmd0O8KgIMKgIMKgJmx0O2hyIG5vc2hhZGUmZ3Q7 PGJyPgomZ3Q7wqAgwqAgwqAmbHQ7ZGl2IGFsaWduPSZxdW90O3JpZ2h0JnF1b3Q7Jmd0O1dTR0kg U2VydmVyJmx0Oy9kaXYmZ3Q7PGJyPgomZ3Q7wqAgwqAmbHQ7L2JvZHkmZ3Q7PGJyPgomZ3Q7ICZs dDsvaHRtbCZndDs8YnI+CiZndDs8YnI+CiZndDsgUmVwb3NpdG9yeSBtZXRhZGF0YSB1cGRhdGVk Ljxicj4KJmd0OyBGYWlsZWQgdG8gdXBkYXRlIGEgcmVwb3NpdG9yeS48YnI+CiZndDs8YnI+CiZn dDsgSSBtaWdodCBoYXZlIGFjY2lkZW50YWxseSBjcmVhdGVkIGEgJnF1b3Q7YmFkJnF1b3Q7IHJl cG9zaXRvcnkgdGhhdCBpcyBsZWFkaW5nIHRvPGJyPgomZ3Q7IHRoaXMgZXJyb3IuIFRoaXMgaXMg d2l0aCB2ZXJzaW9uIDAuMjMuMC4gQWx0ZXJuYXRlbHksIGlzIHRoZXJlIGEgd2F5IHRvPGJyPgom Z3Q7IGRlbGV0ZSB0aGUgdG9vbCBzbyB0aGF0IEkgY2FuIHRyeSBhbmQgcmVjcmVhdGUgaXQ/PGJy PgomZ3Q7PGJyPgomZ3Q7IFRoYW5rcyE8YnI+CiZndDsgUGV0ZXI8YnI+CiZndDs8YnI+CiZndDs8 YnI+CjwvZGl2PjwvZGl2PiZndDsgX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX188YnI+CiZndDsgUGxlYXNlIGtlZXAgYWxsIHJlcGxpZXMg b24gdGhlIGxpc3QgYnkgdXNpbmcgJnF1b3Q7cmVwbHkgYWxsJnF1b3Q7PGJyPgomZ3Q7IGluIHlv dXIgbWFpbCBjbGllbnQuwqAgVG8gbWFuYWdlIHlvdXIgc3Vic2NyaXB0aW9ucyB0byB0aGlzPGJy PgomZ3Q7IGFuZCBvdGhlciBHYWxheHkgbGlzdHMsIHBsZWFzZSB1c2UgdGhlIGludGVyZmFjZSBh dDo8YnI+CiZndDvCoCDCoDxhIGhyZWY9Imh0dHBzOi8vbGlzdHMuZ2FsYXh5cHJvamVjdC5vcmcv IiByZWw9Im5vcmVmZXJyZXIiIHRhcmdldD0iX2JsYW5rIj5odHRwczovL2xpc3RzLmdhbGF4eXBy b2plY3Qub3JnLzwvYT48YnI+CiZndDs8YnI+CiZndDsgVG8gc2VhcmNoIEdhbGF4eSBtYWlsaW5n IGxpc3RzIHVzZSB0aGUgdW5pZmllZCBzZWFyY2ggYXQ6PGJyPgomZ3Q7wqAgwqA8YSBocmVmPSJo dHRwOi8vZ2FsYXh5cHJvamVjdC5vcmcvc2VhcmNoL21haWxpbmdsaXN0cy8iIHJlbD0ibm9yZWZl cnJlciIgdGFyZ2V0PSJfYmxhbmsiPmh0dHA6Ly9nYWxheHlwcm9qZWN0Lm9yZy9zZWFyY2gvbWFp bGluZ2xpc3RzLzwvYT48YnI+CiZndDs8YnI+CjwvYmxvY2txdW90ZT48L2Rpdj48YnI+PC9kaXY+ Cg== --===============8445173521020501086==--