8:48 p.m.
Hello,
Standard CentOS 5.4 install
[root@mako1 scripts]# python -V
Python 2.4.3
Following the instructions
http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
but fails at "sh setup.sh" because "check_python.py" throws and
exeption
and returns "python -ES". Note sure what this means.
thanks
kaizaad
9:14 p.m.
Hi Kaizaad,
Could you provide the exception that is raised?
Thanks,
Kanwei
On Wed, Jan 20, 2010 at 3:48 PM, Kaizaad Bilimorya <kaizaad(a)sharcnet.ca> wrote:
Hello,
Standard CentOS 5.4 install
[root@mako1 scripts]# python -V
Python 2.4.3
Following the instructions
http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
but fails at "sh setup.sh" because "check_python.py" throws and
exeption and
returns "python -ES". Note sure what this means.
thanks
kaizaad
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
9:45 p.m.
Hello Kanwei,
Hmmm, not really. All I know is that setup.sh fails.
$ cd galaxy_dist/
$ sh setup.sh
$ echo $?
1
$ grep -B1 exit setup.sh
CLEAN_PYTHON=`python ./scripts/check_python.py`
[ $? -ne 0 ] && exit 1
$ python ./scripts/check_python.py
python -ES
$ echo $?
1
thanks
kaizaad
On Wed, 20 Jan 2010, Kanwei Li wrote:
Hi Kaizaad,
Could you provide the exception that is raised?
Thanks,
Kanwei
On Wed, Jan 20, 2010 at 3:48 PM, Kaizaad Bilimorya <kaizaad(a)sharcnet.ca> wrote:
> Hello,
>
> Standard CentOS 5.4 install
> [root@mako1 scripts]# python -V
> Python 2.4.3
>
> Following the instructions
> http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
>
> but fails at "sh setup.sh" because "check_python.py" throws and
exeption and
> returns "python -ES". Note sure what this means.
>
> thanks
> kaizaad
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
12:44 a.m.
Kaizaad Bilimorya wrote:
Hello Kanwei,
Hmmm, not really. All I know is that setup.sh fails.
$ cd galaxy_dist/
$ sh setup.sh
$ echo $?
1
$ grep -B1 exit setup.sh
CLEAN_PYTHON=`python ./scripts/check_python.py`
[ $? -ne 0 ] && exit 1
$ python ./scripts/check_python.py
python -ES
$ echo $?
1
Hi Kaizaad,
There was a bug in check_python.py that was fixed shortly after it was
added to the process. Can you check your revision via 'hg id'?
--nate
thanks
kaizaad
On Wed, 20 Jan 2010, Kanwei Li wrote:
> Hi Kaizaad,
>
> Could you provide the exception that is raised?
>
> Thanks,
>
> Kanwei
>
> On Wed, Jan 20, 2010 at 3:48 PM, Kaizaad Bilimorya
> <kaizaad(a)sharcnet.ca> wrote:
>> Hello,
>>
>> Standard CentOS 5.4 install
>> [root@mako1 scripts]# python -V
>> Python 2.4.3
>>
>> Following the instructions
>> http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
>>
>> but fails at "sh setup.sh" because "check_python.py" throws
and
>> exeption and
>> returns "python -ES". Note sure what this means.
>>
>> thanks
>> kaizaad
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
4:16 a.m.
On Wed, 20 Jan 2010, Nate Coraor wrote:
Kaizaad Bilimorya wrote:
> Hello Kanwei,
>
> Hmmm, not really. All I know is that setup.sh fails.
>
> $ cd galaxy_dist/
> $ sh setup.sh
> $ echo $?
> 1
>
> $ grep -B1 exit setup.sh
> CLEAN_PYTHON=`python ./scripts/check_python.py`
> [ $? -ne 0 ] && exit 1
>
> $ python ./scripts/check_python.py
> python -ES
>
> $ echo $?
> 1
Hi Kaizaad,
There was a bug in check_python.py that was fixed shortly after it was added
to the process. Can you check your revision via 'hg id'?
--nate
Hi Nate
I just downloaded it this morning via:
hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
Here is what the id shows:
$ hg id
56efe838b9af tip
thanks
-k
2:33 p.m.
Kaizaad Bilimorya wrote:
Hi Nate
I just downloaded it this morning via:
hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
Here is what the id shows:
$ hg id
56efe838b9af tip
thanks
-k
Hmm, check_python.py really shouldn't be returning 1 there. You could
put a 'raise' after the except line in that file and see what it's throwing.
I hope to do away with both -E and -S in the near future, so we won't
even need this check anymore.
--nate
2:54 p.m.
On Thu, 21 Jan 2010, Nate Coraor wrote:
Kaizaad Bilimorya wrote:
> Hi Nate
>
> I just downloaded it this morning via:
> hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
>
> Here is what the id shows:
> $ hg id
> 56efe838b9af tip
>
> thanks
> -k
Hmm, check_python.py really shouldn't be returning 1 there. You could put a
'raise' after the except line in that file and see what it's throwing.
I hope to do away with both -E and -S in the near future, so we won't even
need this check anymore.
--nate
I think I put it in the right place since it seemed to work, I can
get through the setup now.
Thanks!
-k
--- check_python.py.orig 2010-01-20 14:06:07.000000000 -0500
+++ check_python.py 2010-01-21 09:52:23.000000000 -0500
@@ -26,4 +26,5 @@
print check_virtualenv()
sys.exit( 0 )
except Exception:
+ raise
sys.exit( 1 )
3:14 p.m.
Kaizaad Bilimorya wrote:
I think I put it in the right place since it seemed to work, I can
get
through the setup now.
That's a bit inexplicable as it should still return 1 and in addition,
print an error. Regardless, I'm glad it works now, and as I mentioned,
should be unnecessary soon.
--nate
Thanks!
-k
--- check_python.py.orig 2010-01-20 14:06:07.000000000 -0500
+++ check_python.py 2010-01-21 09:52:23.000000000 -0500
@@ -26,4 +26,5 @@
print check_virtualenv()
sys.exit( 0 )
except Exception:
+ raise
sys.exit( 1 )
4545
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4546
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7 comments
3 participants
participants (3)
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Kaizaad Bilimorya -
Kanwei Li -
Nate Coraor