On 3/12/10 11:33 AM, "Chris Cole" <chris(a)compbio.dundee.ac.uk> wrote:
On 11/03/10 17:01, Nate Coraor wrote:
> Chris Cole wrote:
>
>> Just checked it again (sorry I shouldn't have sent the previous email)
>> with a directory and it still isn't working.
>>
>> www-galaxy@ge-002: tmp> cd ~/data_import/
>> www-galaxy@ge-002: data_import> ls
>> README
>> www-galaxy@ge-002: data_import> ln -s /homes/pschofield/data/TOH
>> www-galaxy@ge-002: data_import> ls TOH/
>> 0min_1.txt 30m_1.txt 60min_1.txt Cd_inuc_1.txt Cmono_1.txt
>> Dd_inuc_1.txt Dmono_1.txt processed
>> 0min_2.txt 30m_2.txt 60min_2.txt Cd_inuc_2.txt Cmono_2.txt
>> Dd_inuc_2.txt Dmono_2.txt
>> www-galaxy@ge-002: data_import> ls -l
>> total 96
>> -rw-r--r-- 1 www-galaxy barton 142 Mar 9 14:14 README
>> lrwxrwxrwx 1 www-galaxy barton 26 Mar 9 15:59 TOH ->
>> /homes/pschofield/data/TOH
>>
>> I got the TOH option in the 'Upload directory of files', which I
>> selected, but the upload failed. Again, this is the error I get when
>> selecting one of the filenames in the dataset:
>> Traceback (most recent call last): File
>> "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line
>> 326, in __main__() File
>> "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line
>> 318, in __main__ add_file( dataset,
>> error
>
> Hi Chris,
>
> Chances are, the files in /homes/pschofield/data/TOH are not writable by
> Galaxy. Galaxy was trying to convert newlines to UNIX on those files as
> part of the import process. This behavior was not intentional.
Yup. That's correct. Galaxy has read-only access to the original files.
This is necessary as users have their own locations for their raw NGS
data which they want to upload to Galaxy.
Hi Nate, Hi Chris
I was hoping this would also explain our weird problem (first mentioned in
my e-mail to the list Jan 21st)...but even if the files are writable by
galaxy it doesn't work, eg:
if I try to import the following files:
(sorry, I have to blank out the full path)
galaxy@erbium:/****/test$ ls -l
total 8
-rw-rw-rw- 1 haruhotz gbioinfo 841 2010-03-14 16:18 P51003.fasta
-rw-r--r-- 1 galaxy galaxy 828 2010-03-14 16:18 P51004.fasta
galaxy@erbium:/****/test$
it doesn't work, with the following error message (for both files):
"
Traceback (most recent call last): File
"/***/galaxy_dist/tools/data_source/upload.py", line 311, in __main__()
File "/***/galaxy_dist/tools/data_source/upload.py", line 302, in __main__
add_fil
error
"
Only if I delete the file P51003.fasta, eg as user galaxy:
galaxy@erbium:/****/test$ rm P51003.fasta
galaxy@erbium:/****/test$ ls -l
total 4
-rw-r--r-- 1 galaxy galaxy 828 2010-03-14 16:18 P51004.fasta
galaxy@erbium:/****/test$
the remaining file get's imported (and I guess 'rewritten' by galaxy):
galaxy@erbium:/****/test$ ls -l
total 4
-rw------- 1 galaxy galaxy 828 2010-03-14 16:26 P51004.fasta
galaxy@erbium:/****/test
Nevertheless, I put my hope into the the next update (including
"3517:0c9e154e9176") which I will do in the next few weeks.
Regard, Hans
> I've just committed 3517:0c9e154e9176, which will prevent
Galaxy from
> ever attempting to modify the import files. When copying in to Galaxy,
> they will still converted, but no longer "in-place" (a temp file is
> used). When not copying (i.e. symlinking), no newline conversion will be
> performed since doing so would require modifying the import file.
Great. I'll look out for the latest updates and try it again, then.
Again, thanks very much for the fixes.
Cheers,
Chris
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