On Thu, Mar 3, 2016 at 12:06 PM, Makis Ladoukakis makis4ever@hotmail.com wrote:

Hello everyone,

I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error:

Traceback (most recent call last): File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in <module> from Bio import SeqIO ImportError: No module named Bio

However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython.

When I type Python and write "from Bio import SeqIO" I get no error.

Can this be an issue related to the virtual environment that is initialized each time Galaxy starts?

Thank you in advance, Makis Ladoukakis

Almost certainly, yes, this is due to the new venv setup in Galaxy.

If you had manually installed Biopython, I would suggest you install it again but inside the venv.

If you installed Biopython via the Tool Shed package, that is more troubling. Try doing a re-install via the Tool Shed.

Peter

Yeah Linda, this was the case for me. When I started the virtual environment I reinstalled BioPython and everything worked again. I suggest you do the same to any packages you need for your tools.

Makis

To: galaxy-dev@lists.galaxyproject.org From: linda.bakker@wur.nl Date: Thu, 3 Mar 2016 14:10:44 +0100 Subject: Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

I guess this relates directly to my question as well...

On 03/03/2016 01:06 PM, Makis Ladoukakis wrote:

Hello everyone,

I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error:

Traceback (most recent call last): File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in <module> from Bio import SeqIO ImportError: No module named Bio

However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython.

When I type Python and write "from Bio import SeqIO" I get no error.

Can this be an issue related to the virtual environment that is initialized each time Galaxy starts?

Thank you in advance,

Makis Ladoukakis

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-- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker@wur.nl

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Good morning Efthymios Ladoukakis

Yes I had this error and after repeated attempts if found out

sh manage_db.sh upgrade because your version is older than the current releaase expects

You get a python vitural env error but

is fixed by running under sudo

sudo sh manage_db.sh

Try that

cheers,

bob

On January 17, 2017 at 7:33 AM Makis Ladoukakis makis4ever@hotmail.com wrote:

Hello everyone,


I tried to download a newer version of Galaxy (I had 15.10 and pulled 16.01 in a different directory) and now for some reason in my old working directory I get the error:


Your database has version '133' but this code expects version '129'.


Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'.





when I tried:




sh manage_db.sh downgrade --version=129




I got the error:



Traceback (most recent call last):
  File "./scripts/manage_db.py", line 33, in <module>
    invoke_migrate_main()
  File "./scripts/manage_db.py", line 30, in invoke_migrate_main
    main( repository=repo, url=db_url )
  File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/shell.py", line 209, in main
    ret = command_func(**kwargs)
  File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py", line 202, in downgrade
    return _migrate(url, repository, version, upgrade=False, err=err, **opts)
  File "<string>", line 2, in _migrate
  File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/util/__init__.py", line 160, in with_engine
    return f(*a, **kw)
  File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py", line 345, in _migrate
    changeset = schema.changeset(version)
  File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py", line 82, in changeset
    changeset = self.repository.changeset(database, start_ver, version)
  File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/repository.py", line 225, in changeset
    changes = [self.version(v).script(database, op) for v in versions]
  File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/repository.py", line 189, in version
    return self.versions.version(*p, **k)
  File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/version.py", line 160, in version
    return self.versions[VerNum(vernum)]
KeyError: <VerNum(133)>






I checked earlier posts stating  that i need to remove all .pyc files before downgrading. I did just that but nothing worked.


Any ideas?


Thank you in advance,

Efthymios Ladoukakis

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Thanks a lot for your help! That actually worked.

Kind regards,

Efthymios Ladoukakis

________________________________ From: Martin Čech marten@bx.psu.edu Sent: Tuesday, January 17, 2017 4:16 PM To: Makis Ladoukakis; galaxy-dev@lists.galaxyproject.org; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Can't downgrade database.

Makis,

you need to run the downgrade command (sh manage_db.sh downgrade --version=129) from the folder with the newer Galaxy. The old one does not have the downgrading scripts.

Thanks for using Galaxy.

Martin

On Tue, Jan 17, 2017 at 7:33 AM Makis Ladoukakis <makis4ever@hotmail.commailto:makis4ever@hotmail.com> wrote:

Hello everyone,

I tried to download a newer version of Galaxy (I had 15.10 and pulled 16.01 in a different directory) and now for some reason in my old working directory I get the error:

Your database has version '133' but this code expects version '129'.

Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'.

when I tried:

sh manage_db.sh downgrade --version=129

I got the error:

Traceback (most recent call last): File "./scripts/manage_db.py", line 33, in <module> invoke_migrate_main() File "./scripts/manage_db.py", line 30, in invoke_migrate_main main( repository=repo, url=db_url ) File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/shell.py", line 209, in main ret = command_func(**kwargs) File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py", line 202, in downgrade return _migrate(url, repository, version, upgrade=False, err=err, **opts) File "<string>", line 2, in _migrate File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/util/__init__.py", line 160, in with_engine return f(*a, **kw) File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py", line 345, in _migrate changeset = schema.changeset(version) File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py", line 82, in changeset changeset = self.repository.changeset(database, start_ver, version) File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/repository.py", line 225, in changeset changes = [self.version(v).script(database, op) for v in versions] File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/repository.py", line 189, in version return self.versions.version(*p, **k) File "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/version.py", line 160, in version return self.versions[VerNum(vernum)] KeyError: <VerNum(133)>

I checked earlier posts stating that i need to remove all .pyc files before downgrading. I did just that but nothing worked.

Any ideas?

Thank you in advance,

Efthymios Ladoukakis

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