Re: [galaxy-dev] Galaxy API to upload files to data library
Perfect. Thanks!
On Fri, Jun 26, 2015 at 6:02 PM, Martin Čech mar...@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 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'
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[galaxy-dev] Error sorting or uploading Bam File
Hi all, My galaxy is the last update and I work with samtools 1.2. I have a bug with the sorting and the upload of bam file. This bug appears only when I try to upload bam sorted by name or when I try to sort by name. When I work with bam sorted by coordinate, there is no problem. So, when I try to sort a bam file by name, this error appears under the bug icon : Tool execution generated the following error message: [bam_sort_core] merging from 20 files... *** Error in `python': double free or corruption (!prev): 0x02897990 *** Aborted (core dumped) The tool produced the following additional output: [E::hts_idx_push] chromosome blocks not continuous Galaxy attempted to build the BAM index with samtools 1.0+ but failed: [Errno 2] No such file or directory: '/data/galaxy-dist/database/job_working_directory/024/24109/__dataset_48619_metadata_temp_file_MqhjBN.bai' And the same type of error appears when I try to upload bam sorted by name. What I understand is that the bam can be sorted properly (The command line to sort is ok in a terminal with no bug and I can follow this step in the job_working_directory during the run) but Galaxy seems to fail to create a bai. For our analysis pipeline, I think the bai is not crucial, is it possible to avoid this creation of bai during uploading and sorting of bam file by name ? Is there another problem than this creation of bai ? Thanks. Julie ___ 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] LDAP and new history creation
Thanks Eric, I’ve tried this this morning. Seems to work like a charm ! Bye, Erwan Le 26 juin 2015 à 16:35, Eric Rasche e...@tamu.edu a écrit : 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 mailto: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/ https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ 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 mailto:e...@tamu.edu rasche.e...@yandex.ru mailto: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/
Re: [galaxy-dev] planemo shed_update - error
Thanks for the bug report. I have fixed this problem here (https://github.com/galaxyproject/planemo/commit/a32d0820a6b856d8d15c9619c97549230a17) and released a new version of planemo (0.13.0) with fix. Hopefully you will get a better error message after the upgrade if there is still a configuration issue. -John On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Alexander, I have opend an issue: https://github.com/galaxyproject/planemo/issues/240 Thanks for reporting, Bjoern Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel: 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/ ___ 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] planemo shed_update - error
Thanks, now I get the following directly after the diff output: Could not update stacks object of type 'NoneType' has no len() /usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) /usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) Repository metadata updated. Failed to update a repository. What does that mean? Best, Alexander 2015-06-29 10:41 GMT-05:00 John Chilton jmchil...@gmail.com: Thanks for the bug report. I have fixed this problem here ( https://github.com/galaxyproject/planemo/commit/a32d0820a6b856d8d15c9619c97549230a17 ) and released a new version of planemo (0.13.0) with fix. Hopefully you will get a better error message after the upgrade if there is still a configuration issue. -John On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Alexander, I have opend an issue: https://github.com/galaxyproject/planemo/issues/240 Thanks for reporting, Bjoern Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel: 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/ ___ 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] planemo shed_update - error
Ay shit. Just realized during looking at it the third time: Someone forgot to uncomment the key line o_o' 2015-06-29 16:21 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com : Here they are: ~/.planemo.yml: http://pastebin.com/nWdT6ybx Command-Log: http://pastebin.com/baBmrD8d 2015-06-29 15:23 GMT-05:00 John Chilton jmchil...@gmail.com: Do you have a ~/.planemo.yml file? I think probably yes based on the previous exception. Can you replace passwords and keys with and send me a copy of that as well as the command-line that produced the above output? -John On Mon, Jun 29, 2015 at 12:05 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Thanks, now I get the following directly after the diff output: Could not update stacks object of type 'NoneType' has no len() /usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) /usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) Repository metadata updated. Failed to update a repository. What does that mean? Best, Alexander 2015-06-29 10:41 GMT-05:00 John Chilton jmchil...@gmail.com: Thanks for the bug report. I have fixed this problem here ( https://github.com/galaxyproject/planemo/commit/a32d0820a6b856d8d15c9619c97549230a17 ) and released a new version of planemo (0.13.0) with fix. Hopefully you will get a better error message after the upgrade if there is still a configuration issue. -John On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Alexander, I have opend an issue: https://github.com/galaxyproject/planemo/issues/240 Thanks for reporting, Bjoern Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel: 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/ ___ 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
Re: [galaxy-dev] planemo shed_update - error
Here they are: ~/.planemo.yml: http://pastebin.com/nWdT6ybx Command-Log: http://pastebin.com/baBmrD8d 2015-06-29 15:23 GMT-05:00 John Chilton jmchil...@gmail.com: Do you have a ~/.planemo.yml file? I think probably yes based on the previous exception. Can you replace passwords and keys with and send me a copy of that as well as the command-line that produced the above output? -John On Mon, Jun 29, 2015 at 12:05 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Thanks, now I get the following directly after the diff output: Could not update stacks object of type 'NoneType' has no len() /usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) /usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) Repository metadata updated. Failed to update a repository. What does that mean? Best, Alexander 2015-06-29 10:41 GMT-05:00 John Chilton jmchil...@gmail.com: Thanks for the bug report. I have fixed this problem here ( https://github.com/galaxyproject/planemo/commit/a32d0820a6b856d8d15c9619c97549230a17 ) and released a new version of planemo (0.13.0) with fix. Hopefully you will get a better error message after the upgrade if there is still a configuration issue. -John On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Alexander, I have opend an issue: https://github.com/galaxyproject/planemo/issues/240 Thanks for reporting, Bjoern Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel: 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/ ___ 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
Re: [galaxy-dev] planemo shed_update - error
Do you have a ~/.planemo.yml file? I think probably yes based on the previous exception. Can you replace passwords and keys with and send me a copy of that as well as the command-line that produced the above output? -John On Mon, Jun 29, 2015 at 12:05 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Thanks, now I get the following directly after the diff output: Could not update stacks object of type 'NoneType' has no len() /usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) /usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) Repository metadata updated. Failed to update a repository. What does that mean? Best, Alexander 2015-06-29 10:41 GMT-05:00 John Chilton jmchil...@gmail.com: Thanks for the bug report. I have fixed this problem here (https://github.com/galaxyproject/planemo/commit/a32d0820a6b856d8d15c9619c97549230a17) and released a new version of planemo (0.13.0) with fix. Hopefully you will get a better error message after the upgrade if there is still a configuration issue. -John On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Alexander, I have opend an issue: https://github.com/galaxyproject/planemo/issues/240 Thanks for reporting, Bjoern Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel: 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/ ___ 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] Download of hg19 genome by data manager fails
Dear All, I have some problems with the download of genome files by the data manager. I tried to download some genome files from the UCSC server with the data manager of galaxy ( name: data_manager_fetch_genome_all_fasta, revision: cca219f2b212), but it fails because of a timeout. Our galaxy server is in an internal network without connection to the Internet. To access the Internet we are required to go trough a http-proxy before any web-services can be accessed. The file /shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py manages the download of the file. Line 183 shows the problem. Here the FTP item from the python ftplib module tries to establishes the connection to the UCSC ftp server. This connection fails. So here is my question: How can i download data by the data manager with a http-proxy? Thanks for help! Tobias ___ 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/
