migratting to Galaxy new realease error
Dear all, I have migrate my old version of Galaxy to the new release V17.01, And I am facing this error when I am running run.sh, any clue ? Installing collected packages: python-ldap Found existing installation: python-ldap 2.4.17 DEPRECATION: Uninstalling a distutils installed project (python-ldap) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Can't uninstall 'python-ldap'. No files were found to uninstall. Can't roll back python-ldap; was not uninstalled Exception: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install **kwargs File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 851, in install self.move_wheel_files(self.source_dir, root=root, prefix=prefix) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 1064, in move_wheel_files isolated=self.isolated, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 345, in move_wheel_files clobber(source, lib_dir, True) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 329, in clobber os.utime(destfile, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/home/galaxy/galaxy-dist/.venv/lib64/python2.7/site-packages/dsml.pyo' Thanks, Mohamed
Hello i tried to install via root and maybe it works, However now the bash run.sh it is working, however my ldap is not working I have password incorrect and I get this error in the terminal : galaxy.auth.providers.ldap_ad ERROR 2017-02-24 10:52:24,672 LDAP authenticate: search exception Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/auth/providers/ldap_ad.py", line 118, in authenticate ldap.set_option(*opt) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 135, in set_option return _ldap_function_call(None,_ldap.set_option,option,invalue) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 66, in _ldap_function_call result = func(*args,**kwargs) ValueError: option error Any idea ? Thanks, Mohamed 2017-02-24 9:11 GMT+01:00 Mohamed Kassam <k.mamoud@gmail.com>:
Dear all,
I have migrate my old version of Galaxy to the new release V17.01, And I am facing this error when I am running run.sh, any clue ?
Installing collected packages: python-ldap Found existing installation: python-ldap 2.4.17 DEPRECATION: Uninstalling a distutils installed project (python-ldap) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Can't uninstall 'python-ldap'. No files were found to uninstall. Can't roll back python-ldap; was not uninstalled Exception: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site- packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install **kwargs File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site- packages/pip/req/req_install.py", line 851, in install self.move_wheel_files(self.source_dir, root=root, prefix=prefix) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site- packages/pip/req/req_install.py", line 1064, in move_wheel_files isolated=self.isolated, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 345, in move_wheel_files clobber(source, lib_dir, True) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 329, in clobber os.utime(destfile, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/home/galaxy/galaxy-dist/. venv/lib64/python2.7/site-packages/dsml.pyo'
Thanks,
Mohamed
Hi Mohamed, Have you try to remove (and backup if you want) the whole .venn folder? Galaxy will create a new one with all its needs. Best Gildas ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/> Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------
Le 24 févr. 2017 à 09:42, Mohamed Kassam <k.mamoud@gmail.com> a écrit :
Hello i tried to install via root and maybe it works,
However now the bash run.sh it is working, however my ldap is not working I have password incorrect and I get this error in the terminal :
galaxy.auth.providers.ldap_ad ERROR 2017-02-24 10:52:24,672 LDAP authenticate: search exception Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/auth/providers/ldap_ad.py", line 118, in authenticate ldap.set_option(*opt) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 135, in set_option return _ldap_function_call(None,_ldap.set_option,option,invalue) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 66, in _ldap_function_call result = func(*args,**kwargs) ValueError: option error
Any idea ?
Thanks,
Mohamed
2017-02-24 9:11 GMT+01:00 Mohamed Kassam <k.mamoud@gmail.com <mailto:k.mamoud@gmail.com>>: Dear all,
I have migrate my old version of Galaxy to the new release V17.01, And I am facing this error when I am running run.sh, any clue ?
Installing collected packages: python-ldap Found existing installation: python-ldap 2.4.17 DEPRECATION: Uninstalling a distutils installed project (python-ldap) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Can't uninstall 'python-ldap'. No files were found to uninstall. Can't roll back python-ldap; was not uninstalled Exception: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install **kwargs File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 851, in install self.move_wheel_files(self.source_dir, root=root, prefix=prefix) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 1064, in move_wheel_files isolated=self.isolated, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 345, in move_wheel_files clobber(source, lib_dir, True) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 329, in clobber os.utime(destfile, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/home/galaxy/galaxy-dist/.venv/lib64/python2.7/site-packages/dsml.pyo'
Thanks,
Mohamed
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Dear Gildas, Thanks for your message. So I 've tried and it recretaed a new .venv. I've checked the ldap python and it was succeffully installed : Installing collected packages: psycopg2, Pygments, WebError, python-ldap Successfully installed Pygments-2.0.2 WebError-0.10.3 psycopg2-2.6.1 python-ldap-2.4.27 Activating virtualenv at .venv But the probelm is still there, and I think it is because there is this new folder auth in galaxy-dist/lib/galaxy/auth/. And maybe it is looking from that File "/home/galaxy/galaxy-dist/lib/galaxy/auth/providers/ldap_ad.py", line 118, in authenticate ldap.set_option(*opt) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 135, in set_option return _ldap_function_call(None,_ldap.set_option,option,invalue) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 66, in _ldap_function_call result = func(*args,**kwargs) ValueError: option error Any one has this error ? Mohamed 2017-02-24 9:47 GMT+01:00 Gildas Le Corguillé <lecorguille@sb-roscoff.fr>:
Hi Mohamed,
Have you try to remove (and backup if you want) the whole .venn folder? Galaxy will create a new one with all its needs.
Best
Gildas
----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr
Member of the Workflow4Metabolomics project http://workflow4metabolomics.org
Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 <02%2098%2029%2023%2081> ------------------------------------------------------------------
Le 24 févr. 2017 à 09:42, Mohamed Kassam <k.mamoud@gmail.com> a écrit :
Hello i tried to install via root and maybe it works,
However now the bash run.sh it is working, however my ldap is not working I have password incorrect and I get this error in the terminal :
galaxy.auth.providers.ldap_ad ERROR 2017-02-24 10:52:24,672 LDAP authenticate: search exception Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/auth/providers/ldap_ad.py", line 118, in authenticate ldap.set_option(*opt) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 135, in set_option return _ldap_function_call(None,_ldap.set_option,option,invalue) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 66, in _ldap_function_call result = func(*args,**kwargs) ValueError: option error
Any idea ?
Thanks,
Mohamed
2017-02-24 9:11 GMT+01:00 Mohamed Kassam <k.mamoud@gmail.com>:
Dear all,
I have migrate my old version of Galaxy to the new release V17.01, And I am facing this error when I am running run.sh, any clue ?
Installing collected packages: python-ldap Found existing installation: python-ldap 2.4.17 DEPRECATION: Uninstalling a distutils installed project (python-ldap) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Can't uninstall 'python-ldap'. No files were found to uninstall. Can't roll back python-ldap; was not uninstalled Exception: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install **kwargs File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 851, in install self.move_wheel_files(self.source_dir, root=root, prefix=prefix) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 1064, in move_wheel_files isolated=self.isolated, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 345, in move_wheel_files clobber(source, lib_dir, True) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 329, in clobber os.utime(destfile, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/home/galaxy/galaxy-dist/.ven v/lib64/python2.7/site-packages/dsml.pyo'
Thanks,
Mohamed
___________________________________________________________ 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/
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Hi Mohamed, the lib/galaxy/auth/ folder is not new at all, there seems to be a problem in your config/auth_conf.xml , what do you have inside <ldap-options> </ldap-options> ? Cheers, Nicola On 24/02/17 08:56, Mohamed Kassam wrote:
Dear Gildas,
Thanks for your message.
So I 've tried and it recretaed a new .venv. I've checked the ldap python and it was succeffully installed : Installing collected packages: psycopg2, Pygments, WebError, python-ldap Successfully installed Pygments-2.0.2 WebError-0.10.3 psycopg2-2.6.1 python-ldap-2.4.27 Activating virtualenv at .venv
But the probelm is still there, and I think it is because there is this new folder auth in galaxy-dist/lib/galaxy/auth/. And maybe it is looking from that File "/home/galaxy/galaxy-dist/lib/galaxy/auth/providers/ldap_ad.py", line 118, in authenticate ldap.set_option(*opt) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 135, in set_option return _ldap_function_call(None,_ldap.set_option,option,invalue) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 66, in _ldap_function_call result = func(*args,**kwargs) ValueError: option error
Any one has this error ?
Mohamed
2017-02-24 9:47 GMT+01:00 Gildas Le Corguillé <lecorguille@sb-roscoff.fr <mailto:lecorguille@sb-roscoff.fr>>:
Hi Mohamed,
Have you try to remove (and backup if you want) the whole .venn folder? Galaxy will create a new one with all its needs.
Best
Gildas
----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr
Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/>
Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 <tel:02%2098%2029%2023%2081> ------------------------------------------------------------------
Le 24 févr. 2017 à 09:42, Mohamed Kassam <k.mamoud@gmail.com <mailto:k.mamoud@gmail.com>> a écrit :
Hello i tried to install via root and maybe it works,
However now the bash run.sh it is working, however my ldap is not working I have password incorrect and I get this error in the terminal :
galaxy.auth.providers.ldap_ad ERROR 2017-02-24 10:52:24,672 LDAP authenticate: search exception Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/auth/providers/ldap_ad.py", line 118, in authenticate ldap.set_option(*opt) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 135, in set_option return _ldap_function_call(None,_ldap.set_option,option,invalue) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py", line 66, in _ldap_function_call result = func(*args,**kwargs) ValueError: option error
Any idea ?
Thanks,
Mohamed
2017-02-24 9:11 GMT+01:00 Mohamed Kassam <k.mamoud@gmail.com <mailto:k.mamoud@gmail.com>>:
Dear all,
I have migrate my old version of Galaxy to the new release V17.01, And I am facing this error when I am running run.sh, any clue ?
Installing collected packages: python-ldap Found existing installation: python-ldap 2.4.17 DEPRECATION: Uninstalling a distutils installed project (python-ldap) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Can't uninstall 'python-ldap'. No files were found to uninstall. Can't roll back python-ldap; was not uninstalled Exception: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install **kwargs File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 851, in install self.move_wheel_files(self.source_dir, root=root, prefix=prefix) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py", line 1064, in move_wheel_files isolated=self.isolated, File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 345, in move_wheel_files clobber(source, lib_dir, True) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", line 329, in clobber os.utime(destfile, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/home/galaxy/galaxy-dist/.venv/lib64/python2.7/site-packages/dsml.pyo'
Thanks,
Mohamed
___________________________________________________________ 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/>
___________________________________________________________ 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/
participants (3)
-
Gildas Le Corguillé -
Mohamed Kassam -
Nicola Soranzo