Re: [galaxy-dev] my.galaxy/toolshed bioblend or install_tool_shed_tools swallows toolshed
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.vandenbeek@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.Tamir@vbcf.ac.at wrote: Hi,
a) short version: instead of: http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_installa...
the tool makes a request to: http://gecko.imp.univie.ac.at/api/repositories/get_ordered_installable_revis...
(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_installa...
=>
["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"
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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....
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.vandenbeek@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.Tamir@vbcf.ac.at wrote: Hi,
a) short version: instead of: http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_installa...
the tool makes a request to: http://gecko.imp.univie.ac.at/api/repositories/get_ordered_installable_revis...
(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_installa...
=>
["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/
I have also added the addition of a trailing slash to ephemeris. Thanks for reporting this.
On Aug 31, 2016 7:43 PM, "Nicola Soranzo" nsoranzo@tiscali.it wrote:
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:
and I use ephemeris
thank you very much, ido
On 30 Aug 2016, at 17:55, Marius van den Beek m.vandenbeek@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.Tamir@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/
galaxy-dev@lists.galaxyproject.org
-
Marius van den Beek -
Nicola Soranzo -
Tamir,Ido