Hi Roberto,
I'm happy you solved your issue, thanks for sharing the
solution!
I'd suggest you open a pull request with the fixes at
https://github.com/galaxyproject/galaxy .

Cheers,
Nicola

Il 25.02.2015
15:07 Roberto Alonso CIPF ha scritto: 

> Hello again :), 
> I have
found the problem, the code that merge the files is this: 
>
galaxy/datatypes/tabular.py:484: cmd = 'egrep -v "^@" %s >> %s' % ( '
'.join(split_files[1:]), output_file ) 
> This concatenates the file
name into the sam file. Just adding "h" it is enough, so it will be like
this: 
> 
> galaxy/datatypes/tabular.py:484: cmd = 'egrep -Hv "^@" %s >>
%s' % ( ' '.join(split_files[1:]), output_file ) 
> Thanks all for your
help, best regards 
> 
> On 25 February 2015 at 12:31, Roberto Alonso
CIPF wrote:
> 
>> Ok, I think I understand the line: 
>> beginning
merge: bwa mem
/home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa
/home/ralonso/galaxy-dist/database/files/000/dataset_8.dat >
/home/ralonso/galaxy-dist/database/files/000/dataset_94.dat 2> /dev/null

>> it refers to the original command, so everything is fine with this
line. The other problem still remains 
>> Regards, sorry for the
confusion 
>> 
>> On 25 February 2015 at 11:40, Roberto Alonso CIPF
wrote:
>> 
>>> Hello again, 
>>> this is something that I consider
important, when I see the log I see this output: 
>>> 
>>>
galaxy.jobs.runners.tasks DEBUG 2015-02-25 11:33:30,989 execution
finished - BEGINNING MERGE: BWA MEM
/home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa
/home/ralonso/galaxy-dist/database/files/000/dataset_8.dat >
/home/ralonso/galaxy-dist/database/files/000/dataset_94.dat 2> /dev/null

>>> I think the merge should be done with samtools. I don't know how is
this programmed in Galaxy, but I didn't indicate anywhere the path to
samtools, is it maybe the problem related with this? 
>>> Thanks a lot,

>>> Regards 
>>> 
>>> On 25 February 2015 at 11:13, Roberto Alonso CIPF
wrote:
>>> 
>>>> Hello, 
>>>> I just changed for the CDATA format, but
the problem still remains. When I split by 2, there is no problem, but
when I go for 3, it happens the problem commented before. Here it is the
link to the sam/bam file: 
>>>>
https://dl.dropboxusercontent.com/u/1669701/ejemplo_split.bam [3] 
>>>>
Best regards 
>>>> 
>>>> On 24 February 2015 at 17:49, Peter Cock
wrote:
>>>> 
>>>>> On Tue, Feb 24, 2015 at 4:43 PM, Roberto Alonso CIPF
wrote:
>>>>> > Hello again,
>>>>> >
>>>>> > first of all thanks for your
help, it is being very useful.
>>>>> >
>>>>> > What I have done up to
now is to copy this method to the class Sequence
>>>>> >
>>>>> > def
get_split_commands_sequential(is_compressed, input_name,
output_name,
>>>>> > start_sequence, sequence_count):
>>>>>> ...
>>>>>>
return [cmd]
>>>>> > get_split_commands_sequential =
>>>>> >
staticmethod(get_split_commands_sequential)
>>>>> >
>>>>> > This is
something that you suggested.
>>>>> 
>>>>> Good.
>>>>> 
>>>>> > When I
run the tool with this configuration:
>>>>> >
>>>>> > 
>>>>> > map with
bwa
>>>>> > > split_mode="number_of_parts">
>>>>> >
>>>>> > 
>>>>> > bwa
mem /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa
>>>>> >
$input > $output 2>/dev/null
>>>>> > 
>>>>> > 
>>>>> > 
>>>>> > 
>>>>> >

>>>>> > 
>>>>> >
>>>>> > 
>>>>> > bwa
>>>>> > 
>>>>> >
>>>>> > 
>>>>>

>>>>> One minor improvement would be to escape the ">" as ">" in
>>>>>
your XML, or use the CDATA approach documented here:
>>>>> 
>>>>>
https://wiki.galaxyproject.org/Tools/BestPractices [2]
>>>>> 
>>>>> >
Everything ends ok, but when I go to check how is the sam, I see that in
the
>>>>> > alingments it is the path of the file, i.e
>>>>> >
example_split.sam:
>>>>> >
/home/ralonso/galaxy-dist/database/job_working_directory/000/90/task_2/dataset_91.dat:SRR098409.1113446
>>>>>
> 4 * 0 0 * * 0 0
>>>>> >
TCTGGGTGAGGGAGTGGGGAGTGGGTTTTTGAGGGTGTGTGAGGATGTGTAAGTGGATGGAAGTAGATTGAATGTT
>>>>>
>
############################################################################
>>>>>
> AS:i:0 XS:i:0
>>>>> >
>>>>> > you know what may be going on?
>>>>> >
If i don't split the file, everything goes correctly.
>>>>> 
>>>>> This
sounds to me like there may be a problem with SAM merging?
>>>>> Could
you share the entire example_split.sam file (e.g. as a gist
>>>>> on
GitHub, or via dropbox)?
>>>>> 
>>>>> Peter
>>>> 
>>>> -- 
>>>> 
>>>>
Roberto Alonso 
>>>> Functional Genomics Unit
>>>> Bioinformatics and
Genomics Department
>>>> Prince Felipe Research Center (CIPF) 
>>>>
C./Eduardo Primo Yúfera (Científic), nº 3
>>>> (junto
Oceanografico)
>>>> 46012 Valencia, Spain
>>>> Tel: +34 963289680 Ext.
1021
>>>> Fax: +34 963289574
>>>> E-Mail: ralo...@cipf.es [5]
>>> 
>>>
-- 
>>> 
>>> Roberto Alonso 
>>> Functional Genomics Unit
>>>
Bioinformatics and Genomics Department
>>> Prince Felipe Research Center
(CIPF) 
>>> C./Eduardo Primo Yúfera (Científic), nº 3
>>> (junto
Oceanografico)
>>> 46012 Valencia, Spain
>>> Tel: +34 963289680 Ext.
1021
>>> Fax: +34 963289574
>>> E-Mail: ralo...@cipf.es [7]
>> 
>> --

>> 
>> Roberto Alonso 
>> Functional Genomics Unit
>> Bioinformatics
and Genomics Department
>> Prince Felipe Research Center (CIPF) 
>>
C./Eduardo Primo Yúfera (Científic), nº 3
>> (junto Oceanografico)
>>
46012 Valencia, Spain
>> Tel: +34 963289680 Ext. 1021
>> Fax: +34
963289574
>> E-Mail: ralo...@cipf.es [9]
> 
> -- 
> 
> Roberto Alonso 
>
Functional Genomics Unit
> Bioinformatics and Genomics Department
>
Prince Felipe Research Center (CIPF) 
> C./Eduardo Primo Yúfera
(Científic), nº 3
> (junto Oceanografico)
> 46012 Valencia, Spain
> Tel:
+34 963289680 Ext. 1021
> Fax: +34 963289574
> E-Mail: ralo...@cipf.es
[11]
  


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