Hi Ido, your analysis is correct, this is what the BioBlend documentation prescribes:
https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#bioblend.galaxy.GalaxyInstance Cheers, Nicola ---- Tamir,Ido ha scritto ---- >It only works when specifying the url like this (http + trailing slash) >otherwise urljoin removes the subdir: >'http://server/subdir/' > >and I use ephemeris > >thank you very much, >ido > >> On 30 Aug 2016, at 17:55, Marius van den Beek <m.vandenb...@gmail.com> wrote: >> >> Hi Ido, >> >> please use ephemeris, it’s as easy as it gets: >> pip install ephemeris >> shed-install -g <galaxy_url> -a <admin_key> -t <tool_list_file>. >> The install_tool_shed_tools.py is deprecated and will not work anymore. >> That said, we haven’t tested installing from toolshed on subdirectories, >> it’s entirely possible that there is a problem. >> I will have a look and let you know. >> >> Best, >> Marius >> >> >> On 30 August 2016 at 17:14, Tamir,Ido <ido.ta...@vbcf.ac.at> wrote: >> Hi, >> >> a) >> short version: >> instead of: >> http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw >> >> the tool makes a request to: >> http://gecko.imp.univie.ac.at/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw >> >> (i.e. galtools is missing) >> >> >> >> >> b) >> long version: >> >> my toolshed is running behind a proxy under: >> my.server/galtools >> >> I use the script install_tool_shed_tools.py via galaxy-ansible-playbook (I >> know of ephemeris but don’t know how to use it yet). >> >> Installing tools from the default toolshed works, but when I try to access >> my own tools I see in nxginx logs >> that the request from the script swallowed the “galtools” part. >> >> But the url is stored correctly in json, and I can get the appropriate >> response when I specify the url in a browser: >> >> http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw >> >> => >> >> ["f663fded0c69", "4aeaa49154f8"] >> >> >> thank you very much for your input, >> ido >> >> >> ansible log: >> ok: [localhost] => (item={u'owner': u'itme', u'tool_shed_url': >> u'gecko.imp.univie.ac.at/galtools', u'tool_panel_section_id': u'ngs_rna', >> u'name': u'shrnaseqw'}) => {"changed": false, "cmd": >> ["/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python", >> "install_tool_shed_tools.py", "-y", "name: shrnaseqw\nowner: >> itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: >> gecko.imp.univie.ac.at/galtools\n", "-a", >> "7e7c8ec27a0a99acee883d2beea8a60b", "-g", "http://127.0.0.1:9098/";], >> "delta": "0:00:00.820941", "end": "2016-08-30 16:55:58.869977", "failed": >> false, "failed_when_result": false, "invocation": {"module_args": >> {"_raw_params": "/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python >> install_tool_shed_tools.py -y \"name: shrnaseqw\nowner: >> itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: >> gecko.imp.univie.ac.at/galtools\n\" -a 7e7c8ec27a0a99acee883d2beea8a60b -g >> http://127.0.0.1:9098/";, "_uses_shell": false, "chdir": >> "/groups/vbcf-ngs/wfsys/galaxy/galaxy", "creates": null, "executable": null, >> "removes": null, "warn": true}, "module_name": "command"}, "item": {"name": >> "shrnaseqw", "owner": "itme", "tool_panel_section_id": "ngs_rna", >> "tool_shed_url": "gecko.imp.univie.ac.at/galtools"}, "rc": 1, "start": >> "2016-08-30 16:55:58.049036", "stderr": "Traceback (most recent call >> last):\n File \"install_tool_shed_tools.py\", line 652, in <module>\n >> install_tools(options)\n File \"install_tool_shed_tools.py\", line 590, in >> install_tools\n (tool['name'], tool['owner'])[-1])\n File >> \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/toolshed/repositories/__init__.py\", >> line 147, in get_ordered_installable_revisions\n r = Client._get(self, >> url=url, params=params)\n File >> \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py\", >> line 147, in _get\n raise >> ConnectionError(msg)\nbioblend.galaxy.client.ConnectionError: GET: error >> 404: '<html>\\r\\n<head><title>404 Not Found</title></head>\\r\\n<body >> bgcolor=\"white\">\\r\\n<center><h1>404 Not >> Found</h1></center>\\r\\n<hr><center>nginx/1.2.1</center>\\r\\n</body>\\r\\n</html>\\r\\n', >> 0 attempts left: None", "stdout": "", "stdout_lines": [], "warnings": []} >> >> nginx: >> ==> error.log <== >> 2016/08/30 16:47:54 [error] 833#0: *442173 open() >> "/etc/nginx/html/api/repositories/get_ordered_installable_revisions" failed >> (2: No such file or directory), client: 10.42.160.35, server: gecko, >> request: "GET >> /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw >> HTTP/1.1", host: "gecko.imp.univie.ac.at" >> >> ==> access.log <== >> 10.42.160.35 - - [30/Aug/2016:16:47:54 +0200] "GET >> /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw >> HTTP/1.1" 404 142 "-" "python-requests/2.8.1” >> >> … this is how it should be: >> >> 10.42.160.51 - - [30/Aug/2016:16:52:54 +0200] "GET >> /galtools/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw >> HTTP/1.1" 200 43 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; >> rv:48.0) Gecko/20100101 Firefox/48.0" >> >> >> ___________________________________________________________ >> 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/
