Re: [galaxy-dev] LDAP and new history creation
I have the same problem with CAS under REMOTE_USER, it's pretty annoying. If you're just using LDAP authentication, you can switch over to the recently added built-in LDAP authentication, and this problem should go away for you Ciao, Eric 2015-06-26 9:24 GMT-05:00 Erwan DELAGE erwan.del...@univ-nantes.fr: Dear all, We have a galaxy instance that uses LDAP for authentication and it works fine. The only problem is that a new history is created each time a user log in. When we disable LDAP to use the classical authentication method, the problem goes away. Any idea of what could happen here ? Thanks Erwan ___ 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/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru ___ 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] LDAP and new history creation
Dear all, We have a galaxy instance that uses LDAP for authentication and it works fine. The only problem is that a new history is created each time a user log in. When we disable LDAP to use the classical authentication method, the problem goes away. Any idea of what could happen here ? Thanks Erwan ___ 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] Galaxy API to upload files to data library
Hello Ryan,
for interacting with libraries through the Bioblend:
http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
for loading data to libraries form the Galaxy's system (e.g. after FTP
upload, or when admin):
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
for uploading new files or importing from HDA:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformat...@gmail.com wrote:
By browsing the api code, I discovered library_contents.py that looks like
it should be used. Why this and not folder_contents.py? There seems to be
overlap of these two. I would expect to upload files to folders within
libraries...
On Thu, Jun 25, 2015 at 2:43 PM, Ryan G ngsbioinformat...@gmail.com
wrote:
Hi all - I'm trying to figure out how to script the ability to upload
data (fastq) files to Galaxy via the API.
I can get the Library's root_folder_id, but am unsure of what the API
call is to upload a file. I'm constructing this dictionary:
data = {}
data['folder_id'] = galaxyFolderId
data['create_type'] = 'file'
data['file_type'] = 'fastq'
data['upload_option'] = 'upload_paths'
data['filesystem_paths'] = fileToUpload
data['link_data_only'] = 'link_to_files'
I assume this is the correct format based on other code I've seen, but
I'm not sure what the actual submit call should be. 'api/libraries/' or
'api/folders'
___
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and other Galaxy lists, please use the interface at:
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___
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Re: [galaxy-dev] Galaxy API to upload files to data library
History Dataset Association. i.e. if you already have the dataset in
history you can very easily import it to a data library.
M.
On Fri, Jun 26, 2015 at 1:23 PM Ryan G ngsbioinformat...@gmail.com wrote:
What is HDA?
Sent from my iPhone
On Jun 26, 2015, at 1:10 PM, Martin Čech mar...@bx.psu.edu wrote:
Hello Ryan,
for interacting with libraries through the Bioblend:
http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
for loading data to libraries form the Galaxy's system (e.g. after FTP
upload, or when admin):
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
for uploading new files or importing from HDA:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformat...@gmail.com
wrote:
By browsing the api code, I discovered library_contents.py that looks
like it should be used. Why this and not folder_contents.py? There seems
to be overlap of these two. I would expect to upload files to folders
within libraries...
On Thu, Jun 25, 2015 at 2:43 PM, Ryan G ngsbioinformat...@gmail.com
wrote:
Hi all - I'm trying to figure out how to script the ability to upload
data (fastq) files to Galaxy via the API.
I can get the Library's root_folder_id, but am unsure of what the API
call is to upload a file. I'm constructing this dictionary:
data = {}
data['folder_id'] = galaxyFolderId
data['create_type'] = 'file'
data['file_type'] = 'fastq'
data['upload_option'] = 'upload_paths'
data['filesystem_paths'] = fileToUpload
data['link_data_only'] = 'link_to_files'
I assume this is the correct format based on other code I've seen, but
I'm not sure what the actual submit call should be. 'api/libraries/' or
'api/folders'
___
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:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy API to upload files to data library
What is HDA?
Sent from my iPhone
On Jun 26, 2015, at 1:10 PM, Martin Čech mar...@bx.psu.edu wrote:
Hello Ryan,
for interacting with libraries through the Bioblend:
http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
for loading data to libraries form the Galaxy's system (e.g. after FTP
upload, or when admin):
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
for uploading new files or importing from HDA:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformat...@gmail.com wrote:
By browsing the api code, I discovered library_contents.py that looks like
it should be used. Why this and not folder_contents.py? There seems to be
overlap of these two. I would expect to upload files to folders within
libraries...
On Thu, Jun 25, 2015 at 2:43 PM, Ryan G ngsbioinformat...@gmail.com wrote:
Hi all - I'm trying to figure out how to script the ability to upload data
(fastq) files to Galaxy via the API.
I can get the Library's root_folder_id, but am unsure of what the API call
is to upload a file. I'm constructing this dictionary:
data = {}
data['folder_id'] = galaxyFolderId
data['create_type'] = 'file'
data['file_type'] = 'fastq'
data['upload_option'] = 'upload_paths'
data['filesystem_paths'] = fileToUpload
data['link_data_only'] = 'link_to_files'
I assume this is the correct format based on other code I've seen, but I'm
not sure what the actual submit call should be. 'api/libraries/' or
'api/folders'
___
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] Galaxy API to upload files to data library
What if the data is not in the history? Ie we received ngs data from an
external source and copied it to a location on our server. I now want to link
to it in Galaxy.
What I was doing previously was entering the file system path through the UX
but we want to automate this a bit and have a script scan Various directories
and import all the *.fastq.gz files while preserving the directory structure.
I have most of the script written but just need to figure out how to link to
the datasets.
Sent from my iPhone
On Jun 26, 2015, at 1:24 PM, Martin Čech mar...@bx.psu.edu wrote:
History Dataset Association. i.e. if you already have the dataset in history
you can very easily import it to a data library.
M.
On Fri, Jun 26, 2015 at 1:23 PM Ryan G ngsbioinformat...@gmail.com wrote:
What is HDA?
Sent from my iPhone
On Jun 26, 2015, at 1:10 PM, Martin Čech mar...@bx.psu.edu wrote:
Hello Ryan,
for interacting with libraries through the Bioblend:
http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
for loading data to libraries form the Galaxy's system (e.g. after FTP
upload, or when admin):
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
for uploading new files or importing from HDA:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformat...@gmail.com
wrote:
By browsing the api code, I discovered library_contents.py that looks like
it should be used. Why this and not folder_contents.py? There seems to
be overlap of these two. I would expect to upload files to folders within
libraries...
On Thu, Jun 25, 2015 at 2:43 PM, Ryan G ngsbioinformat...@gmail.com
wrote:
Hi all - I'm trying to figure out how to script the ability to upload
data (fastq) files to Galaxy via the API.
I can get the Library's root_folder_id, but am unsure of what the API
call is to upload a file. I'm constructing this dictionary:
data = {}
data['folder_id'] = galaxyFolderId
data['create_type'] = 'file'
data['file_type'] = 'fastq'
data['upload_option'] = 'upload_paths'
data['filesystem_paths'] = fileToUpload
data['link_data_only'] = 'link_to_files'
I assume this is the correct format based on other code I've seen, but
I'm not sure what the actual submit call should be. 'api/libraries/' or
'api/folders'
___
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:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Galaxy API to upload files to data library
The second link leads to an endpoint that does exactly that.
M.
On Fri, Jun 26, 2015 at 4:43 PM Ryan G ngsbioinformat...@gmail.com wrote:
What if the data is not in the history? Ie we received ngs data from an
external source and copied it to a location on our server. I now want to
link to it in Galaxy.
What I was doing previously was entering the file system path through the
UX but we want to automate this a bit and have a script scan Various
directories and import all the *.fastq.gz files while preserving the
directory structure. I have most of the script written but just need to
figure out how to link to the datasets.
Sent from my iPhone
On Jun 26, 2015, at 1:24 PM, Martin Čech mar...@bx.psu.edu wrote:
History Dataset Association. i.e. if you already have the dataset in
history you can very easily import it to a data library.
M.
On Fri, Jun 26, 2015 at 1:23 PM Ryan G ngsbioinformat...@gmail.com
wrote:
What is HDA?
Sent from my iPhone
On Jun 26, 2015, at 1:10 PM, Martin Čech mar...@bx.psu.edu wrote:
Hello Ryan,
for interacting with libraries through the Bioblend:
http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
for loading data to libraries form the Galaxy's system (e.g. after FTP
upload, or when admin):
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
for uploading new files or importing from HDA:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformat...@gmail.com
wrote:
By browsing the api code, I discovered library_contents.py that looks
like it should be used. Why this and not folder_contents.py? There seems
to be overlap of these two. I would expect to upload files to folders
within libraries...
On Thu, Jun 25, 2015 at 2:43 PM, Ryan G ngsbioinformat...@gmail.com
wrote:
Hi all - I'm trying to figure out how to script the ability to upload
data (fastq) files to Galaxy via the API.
I can get the Library's root_folder_id, but am unsure of what the API
call is to upload a file. I'm constructing this dictionary:
data = {}
data['folder_id'] = galaxyFolderId
data['create_type'] = 'file'
data['file_type'] = 'fastq'
data['upload_option'] = 'upload_paths'
data['filesystem_paths'] = fileToUpload
data['link_data_only'] = 'link_to_files'
I assume this is the correct format based on other code I've seen, but
I'm not sure what the actual submit call should be. 'api/libraries/' or
'api/folders'
___
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] Set build when discovering output in collection
Hi, as many of you probably know by now, I have a tool that creates an output collection by discovering the datasets in this collection like propsed there: [1] Specifically I have a fastq input with set build information (a ref genome). The output is a collection of fastq files. After I managed to give them the same format like the input (hacky version), I now want them to adopt the build ID. How can I do that? Thanks, Alexander [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to-explicitly-produce-dataset/diff ___ 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] Set build when discovering output in collection
FOR GOD'S SAKE SEARCH THE ARCHIVE !!! http://dev.list.galaxyproject.org/Database-Build-td4140140.html https://github.com/galaxyproject/tools-devteam/blob/master/tools/tophat2/tophat2_wrapper.xml#L313 2015-06-26 21:58 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com : Hi, as many of you probably know by now, I have a tool that creates an output collection by discovering the datasets in this collection like propsed there: [1] Specifically I have a fastq input with set build information (a ref genome). The output is a collection of fastq files. After I managed to give them the same format like the input (hacky version), I now want them to adopt the build ID. How can I do that? Thanks, Alexander [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to-explicitly-produce-dataset/diff ___ 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] Set build when discovering output in collection
And the corresponding pull request: https://github.com/galaxyproject/tools-devteam/pull/173 The BWA github-repo is newer than what is on the toolshed, right? When do you update the toolshed? Best, Alexander 2015-06-26 22:17 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com : FOR GOD'S SAKE SEARCH THE ARCHIVE !!! http://dev.list.galaxyproject.org/Database-Build-td4140140.html https://github.com/galaxyproject/tools-devteam/blob/master/tools/tophat2/tophat2_wrapper.xml#L313 2015-06-26 21:58 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com: Hi, as many of you probably know by now, I have a tool that creates an output collection by discovering the datasets in this collection like propsed there: [1] Specifically I have a fastq input with set build information (a ref genome). The output is a collection of fastq files. After I managed to give them the same format like the input (hacky version), I now want them to adopt the build ID. How can I do that? Thanks, Alexander [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to-explicitly-produce-dataset/diff ___ 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] planemo shed_update - error
Hi, I'm running: planemo shed_update --check_diff --shed_target toolshed and get a python error message (see below). shed_diff and shed_lint are working fine. planemo, version 0.12.2 Best, Alexander Traceback (most recent call last): File /usr/local/bin/planemo, line 11, in module sys.exit(planemo()) File /usr/local/lib/python2.7/dist-packages/click/core.py, line 664, in __call__ return self.main(*args, **kwargs) File /usr/local/lib/python2.7/dist-packages/click/core.py, line 644, in main rv = self.invoke(ctx) File /usr/local/lib/python2.7/dist-packages/click/core.py, line 991, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File /usr/local/lib/python2.7/dist-packages/click/core.py, line 837, in invoke return ctx.invoke(self.callback, **ctx.params) File /usr/local/lib/python2.7/dist-packages/click/core.py, line 464, in invoke return callback(*args, **kwargs) File /usr/local/lib/python2.7/dist-packages/click/decorators.py, line 64, in new_func return ctx.invoke(f, obj, *args[1:], **kwargs) File /usr/local/lib/python2.7/dist-packages/click/core.py, line 464, in invoke return callback(*args, **kwargs) File /usr/local/lib/python2.7/dist-packages/planemo/commands/cmd_shed_update.py, line 52, in cli tsi = shed.tool_shed_client(ctx, **kwds) File /usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py, line 331, in tool_shed_client key = prop(key) File /usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py, line 323, in prop return kwds.get(shed_%s % key, None) or shed_config.get(key, None) AttributeError: 'NoneType' object has no attribute 'get' ___ 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/
