Hi, I just did an hg pull for the latest version and I've got errors trying to run the 'Fastq Groomer' and 'Fastq Summary Statistics' tools. It looks like they're related. The old Fastq Groomer as found in the 'Deprecated' tools section works fine. Groomer: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_groomer.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax Summary Stats: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_stats.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax Is this a problem at my end or in Galaxy itself? This is python 2.6, BTW. Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096
Hi Chris, I was unable to reproduce this error using python 2.6 on my system, but I have made the fastqAggregator a new style class in rev. 3487:b4dc8ea68ac. Because I cannot reproduce this error, I am not sure if this will have any effect on the problem you are seeing. If it doesn't fix your issue, can you provide more information about your system setup. Thanks, Dan On Mar 5, 2010, at 8:47 AM, Chris Cole wrote:
Hi,
I just did an hg pull for the latest version and I've got errors trying to run the 'Fastq Groomer' and 'Fastq Summary Statistics' tools. It looks like they're related. The old Fastq Groomer as found in the 'Deprecated' tools section works fine.
Groomer: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_groomer.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax
Summary Stats: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_stats.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax
Is this a problem at my end or in Galaxy itself? This is python 2.6, BTW. Cheers,
Chris
-- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK
url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721
The University of Dundee is a registered Scottish charity, No: SC015096 _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Dan, I can't see that revision. I'm at 3476:adda1b9e31fa with no more changes available via hg pull. What kind of info do you want? I'm running on Linux Centos 5.2 server with python 2.6.4 and MySQL 5.0.45. Anything else? thanks, Chris On 03/05/2010 03:19 PM, Daniel Blankenberg wrote:
Hi Chris,
I was unable to reproduce this error using python 2.6 on my system, but I have made the fastqAggregator a new style class in rev. 3487:b4dc8ea68ac. Because I cannot reproduce this error, I am not sure if this will have any effect on the problem you are seeing. If it doesn't fix your issue, can you provide more information about your system setup.
Thanks,
Dan
On Mar 5, 2010, at 8:47 AM, Chris Cole wrote:
Hi,
I just did an hg pull for the latest version and I've got errors trying to run the 'Fastq Groomer' and 'Fastq Summary Statistics' tools. It looks like they're related. The old Fastq Groomer as found in the 'Deprecated' tools section works fine.
Groomer: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_groomer.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax
Summary Stats: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_stats.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax
Is this a problem at my end or in Galaxy itself? This is python 2.6, BTW. Cheers,
Chris
-- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK
url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721
The University of Dundee is a registered Scottish charity, No: SC015096 _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Chris, we've pushed out change set 3489:3563fade2c86 to the public distrbution now, so this should now be available. On Mar 8, 2010, at 10:16 AM, Chris Cole wrote:
Hi Dan,
I can't see that revision. I'm at 3476:adda1b9e31fa with no more changes available via hg pull.
What kind of info do you want? I'm running on Linux Centos 5.2 server with python 2.6.4 and MySQL 5.0.45. Anything else? thanks,
Chris
On 03/05/2010 03:19 PM, Daniel Blankenberg wrote:
Hi Chris,
I was unable to reproduce this error using python 2.6 on my system, but I have made the fastqAggregator a new style class in rev. 3487:b4dc8ea68ac. Because I cannot reproduce this error, I am not sure if this will have any effect on the problem you are seeing. If it doesn't fix your issue, can you provide more information about your system setup.
Thanks,
Dan
On Mar 5, 2010, at 8:47 AM, Chris Cole wrote:
Hi,
I just did an hg pull for the latest version and I've got errors trying to run the 'Fastq Groomer' and 'Fastq Summary Statistics' tools. It looks like they're related. The old Fastq Groomer as found in the 'Deprecated' tools section works fine.
Groomer: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_groomer.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax
Summary Stats: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_stats.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax
Is this a problem at my end or in Galaxy itself? This is python 2.6, BTW. Cheers,
Chris
-- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK
url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721
The University of Dundee is a registered Scottish charity, No: SC015096 _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi Greg, Thanks. That fixed it. Cheers, Chris On 03/08/2010 04:16 PM, Greg Von Kuster wrote:
Chris, we've pushed out change set 3489:3563fade2c86 to the public distrbution now, so this should now be available.
On Mar 8, 2010, at 10:16 AM, Chris Cole wrote:
Hi Dan,
I can't see that revision. I'm at 3476:adda1b9e31fa with no more changes available via hg pull.
What kind of info do you want? I'm running on Linux Centos 5.2 server with python 2.6.4 and MySQL 5.0.45. Anything else? thanks,
Chris
On 03/05/2010 03:19 PM, Daniel Blankenberg wrote:
Hi Chris,
I was unable to reproduce this error using python 2.6 on my system, but I have made the fastqAggregator a new style class in rev. 3487:b4dc8ea68ac. Because I cannot reproduce this error, I am not sure if this will have any effect on the problem you are seeing. If it doesn't fix your issue, can you provide more information about your system setup.
Thanks,
Dan
On Mar 5, 2010, at 8:47 AM, Chris Cole wrote:
Hi,
I just did an hg pull for the latest version and I've got errors trying to run the 'Fastq Groomer' and 'Fastq Summary Statistics' tools. It looks like they're related. The old Fastq Groomer as found in the 'Deprecated' tools section works fine.
Groomer: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_groomer.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax
Summary Stats: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_stats.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax
Is this a problem at my end or in Galaxy itself? This is python 2.6, BTW. Cheers,
Chris
-- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK
url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721
The University of Dundee is a registered Scottish charity, No: SC015096 _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
participants (3)
-
Chris Cole -
Daniel Blankenberg -
Greg Von Kuster