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'????
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 ngsbioinformatics@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'????
Hello Ryan,
for interacting with libraries through the Bioblend: http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bi...
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/a...
for uploading new files or importing from HDA: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/a...
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformatics@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 ngsbioinformatics@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/
What is HDA?
Sent from my iPhone
On Jun 26, 2015, at 1:10 PM, Martin Čech marten@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-bi...
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/a...
for uploading new files or importing from HDA: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/a...
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformatics@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 ngsbioinformatics@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/
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 ngsbioinformatics@gmail.com wrote:
What is HDA?
Sent from my iPhone
On Jun 26, 2015, at 1:10 PM, Martin Čech marten@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-bi...
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/a...
for uploading new files or importing from HDA:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/a...
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformatics@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 ngsbioinformatics@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/
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 marten@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 ngsbioinformatics@gmail.com wrote: What is HDA?
Sent from my iPhone
On Jun 26, 2015, at 1:10 PM, Martin Čech marten@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-bi...
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/a...
for uploading new files or importing from HDA: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/a...
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformatics@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 ngsbioinformatics@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/
The second link leads to an endpoint that does exactly that. M.
On Fri, Jun 26, 2015 at 4:43 PM Ryan G ngsbioinformatics@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 marten@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 ngsbioinformatics@gmail.com wrote:
What is HDA?
Sent from my iPhone
On Jun 26, 2015, at 1:10 PM, Martin Čech marten@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-bi...
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/a...
for uploading new files or importing from HDA:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/a...
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformatics@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 ngsbioinformatics@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/
Perfect. Thanks!
On Fri, Jun 26, 2015 at 6:02 PM, Martin Čech marten@bx.psu.edu wrote:
The second link leads to an endpoint that does exactly that. M.
On Fri, Jun 26, 2015 at 4:43 PM Ryan G ngsbioinformatics@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 marten@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 ngsbioinformatics@gmail.com wrote:
What is HDA?
Sent from my iPhone
On Jun 26, 2015, at 1:10 PM, Martin Čech marten@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-bi...
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/a...
for uploading new files or importing from HDA:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/a...
Hope this helps.
M.
On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformatics@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 ngsbioinformatics@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/
galaxy-dev@lists.galaxyproject.org
-
Martin Čech -
Ryan G