Hello,
I have tried to install the last version of Bismark from the toolshed and I got an error while installing. Basically it can't install bowtie and bowtie2 because the folder name is written twice in the download directory. Here is the error:
File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 142, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package initial_download=True ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download extraction_path = archive.extract( install_dir ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract os.chmod( absolute_filepath, unix_permissions )
[Errno 2] No such file or directory: './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/'
As you see "bowtie-0.12.8" is twice in the path and when I check the directory, the last "bowtie-0.12.8" folder doesn't exists.
Do you know what could go wrong or an alternative way of specifying the correct path?
Best regards,
Jose
Hi Jose,
which version of Galaxy are you using? @Dave can this be one of the old un-compressing changes?
Cheers, Bjoern
Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro Armenteros:
Hello,
I have tried to install the last version of Bismark from the toolshed and I got an error while installing. Basically it can't install bowtie and bowtie2 because the folder name is written twice in the download directory. Here is the error:
File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 142, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package initial_download=True ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download extraction_path = archive.extract( install_dir ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract os.chmod( absolute_filepath, unix_permissions )
[Errno 2] No such file or directory: './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/'
As you see "bowtie-0.12.8" is twice in the path and when I check the directory, the last "bowtie-0.12.8" folder doesn't exists.
Do you know what could go wrong or an alternative way of specifying the correct path?
Best regards,
Jose
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/
Hello Björn,
I am using Galaxy 15.07, so everything should be updated.
Regards,
Jose
2015-10-28 15:43 GMT+01:00 Björn Grüning bjoern.gruening@gmail.com:
Hi Jose,
which version of Galaxy are you using? @Dave can this be one of the old un-compressing changes?
Cheers, Bjoern
Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro Armenteros:
Hello,
I have tried to install the last version of Bismark from the toolshed
and I
got an error while installing. Basically it can't install bowtie and bowtie2 because the folder name is written twice in the download directory. Here is the error:
File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 142, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 100, in install_and_build_package initial_download=True ) File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
line 32, in execute_step initial_download=initial_download ) File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 685, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 223, in url_download extraction_path = archive.extract( install_dir ) File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 89, in extract os.chmod( absolute_filepath, unix_permissions )
[Errno 2] No such file or directory: './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/'
As you see "bowtie-0.12.8" is twice in the path and when I check the directory, the last "bowtie-0.12.8" folder doesn't exists.
Do you know what could go wrong or an alternative way of specifying the correct path?
Best regards,
Jose
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/
Hi Jose, can you check that your release_15.07 is updated and contains git commit 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc ( https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c23... )?
Cheers, Nicola
On 28/10/15 14:53, Jose Juan Almagro Armenteros wrote:
Hello Björn,
I am using Galaxy 15.07, so everything should be updated.
Regards,
Jose
2015-10-28 15:43 GMT+01:00 Björn Grüning <bjoern.gruening@gmail.com mailto:bjoern.gruening@gmail.com>:
Hi Jose, which version of Galaxy are you using? @Dave can this be one of the old un-compressing changes? Cheers, Bjoern Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro Armenteros: > Hello, > > I have tried to install the last version of Bismark from the toolshed and I > got an error while installing. Basically it can't install bowtie and > bowtie2 because the folder name > is written twice in the download directory. Here is the error: > > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 142, in install_and_build_package_via_fabric > tool_dependency = self.install_and_build_package( > tool_shed_repository, tool_dependency, actions_dict ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 100, in install_and_build_package > initial_download=True ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", > line 32, in execute_step > initial_download=initial_download ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 685, in execute_step > dir = self.url_download( work_dir, downloaded_filename, url, > extract=True, checksums=checksums ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 223, in url_download > extraction_path = archive.extract( install_dir ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 89, in extract > os.chmod( absolute_filepath, unix_permissions ) > > [Errno 2] No such file or directory: > './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/' > > As you see "bowtie-0.12.8" is twice in the path and when I check the > directory, the last "bowtie-0.12.8" folder doesn't exists. > > Do you know what could go wrong or an alternative way of specifying the > correct path? > > > Best regards, > > Jose > > > > ___________________________________________________________ > 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/
Yes, this is definitely related to the issue I fixed part of, and (I think) Nicola fixed the rest of.
- Dave Bouvier http://galaxyproject.org http://usegalaxy.org
On 10/28/2015 11:46 AM, Nicola Soranzo wrote:
Hi Jose, can you check that your release_15.07 is updated and contains git commit 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc ( https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c23... )?
Cheers, Nicola
On 28/10/15 14:53, Jose Juan Almagro Armenteros wrote:
Hello Björn,
I am using Galaxy 15.07, so everything should be updated.
Regards,
Jose
2015-10-28 15:43 GMT+01:00 Björn Grüning <bjoern.gruening@gmail.com mailto:bjoern.gruening@gmail.com>:
Hi Jose, which version of Galaxy are you using? @Dave can this be one of the old un-compressing changes? Cheers, Bjoern Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro Armenteros: > Hello, > > I have tried to install the last version of Bismark from the toolshed and I > got an error while installing. Basically it can't install bowtie and > bowtie2 because the folder name > is written twice in the download directory. Here is the error: > > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 142, in install_and_build_package_via_fabric > tool_dependency = self.install_and_build_package( > tool_shed_repository, tool_dependency, actions_dict ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 100, in install_and_build_package > initial_download=True ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", > line 32, in execute_step > initial_download=initial_download ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 685, in execute_step > dir = self.url_download( work_dir, downloaded_filename, url, > extract=True, checksums=checksums ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 223, in url_download > extraction_path = archive.extract( install_dir ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 89, in extract > os.chmod( absolute_filepath, unix_permissions ) > > [Errno 2] No such file or directory: > './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/' > > As you see "bowtie-0.12.8" is twice in the path and when I check the > directory, the last "bowtie-0.12.8" folder doesn't exists. > > Do you know what could go wrong or an alternative way of specifying the > correct path? > > > Best regards, > > Jose > > > > ___________________________________________________________ > 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/
Hello again,
I have the release_15.07 from Bitbucket, so if I want to have that commit I suppose that I would have to switch my Galaxy instance from Bitbucket to Github. Is this correct?
Regards,
Jose
2015-10-28 17:00 GMT+01:00 Dave Bouvier dave@bx.psu.edu:
Yes, this is definitely related to the issue I fixed part of, and (I think) Nicola fixed the rest of.
Dave Bouvier http://galaxyproject.org http://usegalaxy.org
On 10/28/2015 11:46 AM, Nicola Soranzo wrote:
Hi Jose, can you check that your release_15.07 is updated and contains git commit 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc (
https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c23... )?
Cheers, Nicola
On 28/10/15 14:53, Jose Juan Almagro Armenteros wrote:
Hello Björn,
I am using Galaxy 15.07, so everything should be updated.
Regards,
Jose
2015-10-28 15:43 GMT+01:00 Björn Grüning <bjoern.gruening@gmail.com mailto:bjoern.gruening@gmail.com>:
Hi Jose, which version of Galaxy are you using? @Dave can this be one of the old un-compressing changes? Cheers, Bjoern Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro Armenteros: > Hello, > > I have tried to install the last version of Bismark from the toolshed and I > got an error while installing. Basically it can't install bowtieand > bowtie2 because the folder name > is written twice in the download directory. Here is the error: > > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 142, in install_and_build_package_via_fabric > tool_dependency = self.install_and_build_package( > tool_shed_repository, tool_dependency, actions_dict ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 100, in install_and_build_package > initial_download=True ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", > line 32, in execute_step > initial_download=initial_download ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 685, in execute_step > dir = self.url_download( work_dir, downloaded_filename, url, > extract=True, checksums=checksums ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 223, in url_download > extraction_path = archive.extract( install_dir ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 89, in extract > os.chmod( absolute_filepath, unix_permissions ) > > [Errno 2] No such file or directory: > './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/' > > As you see "bowtie-0.12.8" is twice in the path and when I check the > directory, the last "bowtie-0.12.8" folder doesn't exists. > > Do you know what could go wrong or an alternative way of specifying the > correct path? > > > Best regards, > > Jose > > > > ___________________________________________________________ > 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/
Hi Jose,
I think that is a good idea. Please see the bottom of this page for some hints: https://wiki.galaxyproject.org/Develop/SourceCode
Martin
On Wed, Oct 28, 2015 at 12:06 PM Jose Juan Almagro Armenteros < jjalmagro@gmail.com> wrote:
Hello again,
I have the release_15.07 from Bitbucket, so if I want to have that commit I suppose that I would have to switch my Galaxy instance from Bitbucket to Github. Is this correct?
Regards,
Jose
2015-10-28 17:00 GMT+01:00 Dave Bouvier dave@bx.psu.edu:
Yes, this is definitely related to the issue I fixed part of, and (I think) Nicola fixed the rest of.
Dave Bouvier http://galaxyproject.org http://usegalaxy.org
On 10/28/2015 11:46 AM, Nicola Soranzo wrote:
Hi Jose, can you check that your release_15.07 is updated and contains git commit 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc (
https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c23... )?
Cheers, Nicola
On 28/10/15 14:53, Jose Juan Almagro Armenteros wrote:
Hello Björn,
I am using Galaxy 15.07, so everything should be updated.
Regards,
Jose
2015-10-28 15:43 GMT+01:00 Björn Grüning <bjoern.gruening@gmail.com mailto:bjoern.gruening@gmail.com>:
Hi Jose, which version of Galaxy are you using? @Dave can this be one of the old un-compressing changes? Cheers, Bjoern Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro Armenteros: > Hello, > > I have tried to install the last version of Bismark from the toolshed and I > got an error while installing. Basically it can't install bowtieand > bowtie2 because the folder name > is written twice in the download directory. Here is the error: > > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 142, in install_and_build_package_via_fabric > tool_dependency = self.install_and_build_package( > tool_shed_repository, tool_dependency, actions_dict ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 100, in install_and_build_package > initial_download=True ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", > line 32, in execute_step > initial_download=initial_download ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 685, in execute_step > dir = self.url_download( work_dir, downloaded_filename, url, > extract=True, checksums=checksums ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 223, in url_download > extraction_path = archive.extract( install_dir ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 89, in extract > os.chmod( absolute_filepath, unix_permissions ) > > [Errno 2] No such file or directory: > './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/' > > As you see "bowtie-0.12.8" is twice in the path and when I check the > directory, the last "bowtie-0.12.8" folder doesn't exists. > > Do you know what could go wrong or an alternative way of specifying the > correct path? > > > Best regards, > > Jose > > > > ___________________________________________________________ > 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/
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/
Hi Jose, unfortunately the release_15.07 branch on Bitbucket seems to be missing all post-release updates, and I warmly suggest you to move to the Github releases as soon as you can.
The migration is documented at https://wiki.galaxyproject.org/Admin/SwitchingToGithubFromBitbucket
Cheers, Nicola
On 28/10/15 16:06, Jose Juan Almagro Armenteros wrote:
Hello again,
I have the from Bitbucket, so if I want to have that commit I suppose that I would have to switch my Galaxy instance from Bitbucket to Github. Is this correct?
Regards,
Jose
2015-10-28 17:00 GMT+01:00 Dave Bouvier <dave@bx.psu.edu mailto:dave@bx.psu.edu>:
Yes, this is definitely related to the issue I fixed part of, and (I think) Nicola fixed the rest of. - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 10/28/2015 11:46 AM, Nicola Soranzo wrote: Hi Jose, can you check that your release_15.07 is updated and contains git commit 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc ( https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c232a2b88523fc )? Cheers, Nicola On 28/10/15 14:53, Jose Juan Almagro Armenteros wrote: Hello Björn, I am using Galaxy 15.07, so everything should be updated. Regards, Jose 2015-10-28 15:43 GMT+01:00 Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com> <mailto:bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>>>: Hi Jose, which version of Galaxy are you using? @Dave can this be one of the old un-compressing changes? Cheers, Bjoern Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro Armenteros: > Hello, > > I have tried to install the last version of Bismark from the toolshed and I > got an error while installing. Basically it can't install bowtie and > bowtie2 because the folder name > is written twice in the download directory. Here is the error: > > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 142, in install_and_build_package_via_fabric > tool_dependency = self.install_and_build_package( > tool_shed_repository, tool_dependency, actions_dict ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 100, in install_and_build_package > initial_download=True ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", > line 32, in execute_step > initial_download=initial_download ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 685, in execute_step > dir = self.url_download( work_dir, downloaded_filename, url, > extract=True, checksums=checksums ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 223, in url_download > extraction_path = archive.extract( install_dir ) > File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 89, in extract > os.chmod( absolute_filepath, unix_permissions ) > > [Errno 2] No such file or directory: > './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/' > > As you see "bowtie-0.12.8" is twice in the path and when I check the > directory, the last "bowtie-0.12.8" folder doesn't exists. > > Do you know what could go wrong or an alternative way of specifying the > correct path? > > > Best regards, > > Jose > > > > ___________________________________________________________ > 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/
OK, I will try to switch to Github then.
Thank you for the help!
Regards,
Jose
2015-10-28 17:20 GMT+01:00 Nicola Soranzo nsoranzo@tiscali.it:
Hi Jose, unfortunately the release_15.07 branch on Bitbucket seems to be missing all post-release updates, and I warmly suggest you to move to the Github releases as soon as you can.
The migration is documented at https://wiki.galaxyproject.org/Admin/SwitchingToGithubFromBitbucket
Cheers, Nicola
On 28/10/15 16:06, Jose Juan Almagro Armenteros wrote:
Hello again,
I have the from Bitbucket, so if I want to have that commit I suppose that I would have to switch my Galaxy instance from Bitbucket to Github. Is this correct?
Regards,
Jose
2015-10-28 17:00 GMT+01:00 Dave Bouvier dave@bx.psu.edu:
Yes, this is definitely related to the issue I fixed part of, and (I think) Nicola fixed the rest of.
Dave Bouvier http://galaxyproject.org http://usegalaxy.org
On 10/28/2015 11:46 AM, Nicola Soranzo wrote:
Hi Jose, can you check that your release_15.07 is updated and contains git commit 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc (
https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c23... )?
Cheers, Nicola
On 28/10/15 14:53, Jose Juan Almagro Armenteros wrote:
Hello Björn,
I am using Galaxy 15.07, so everything should be updated.
Regards,
Jose
2015-10-28 15:43 GMT+01:00 Björn Grüning < bjoern.gruening@gmail.com bjoern.gruening@gmail.com mailto:bjoern.gruening@gmail.com>:
Hi Jose, which version of Galaxy are you using? @Dave can this be one of the old un-compressing changes? Cheers, Bjoern Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro Armenteros: > Hello, > > I have tried to install the last version of Bismark from the toolshed and I > got an error while installing. Basically it can't install bowtieand > bowtie2 because the folder name > is written twice in the download directory. Here is the error: > > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 142, in install_and_build_package_via_fabric > tool_dependency = self.install_and_build_package( > tool_shed_repository, tool_dependency, actions_dict ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 100, in install_and_build_package > initial_download=True ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", > line 32, in execute_step > initial_download=initial_download ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 685, in execute_step > dir = self.url_download( work_dir, downloaded_filename, url, > extract=True, checksums=checksums ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 223, in url_download > extraction_path = archive.extract( install_dir ) > File
"/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 89, in extract > os.chmod( absolute_filepath, unix_permissions ) > > [Errno 2] No such file or directory: > './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/' > > As you see "bowtie-0.12.8" is twice in the path and when I check the > directory, the last "bowtie-0.12.8" folder doesn't exists. > > Do you know what could go wrong or an alternative way of specifying the > correct path? > > > Best regards, > > Jose > > > > ___________________________________________________________ > 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@lists.galaxyproject.org
-
Björn Grüning -
Dave Bouvier -
Jose Juan Almagro Armenteros -
Martin Čech -
Nicola Soranzo