Perfect, Galaxy will also need to add the function that was deleted by
merge, in
*galaxy/datatypes/sequence.py:206*:

def get_split_commands_sequential(is_compressed, input_name, output_name,
start_sequence, sequence_count):
        """
        Does a brain-dead sequential scan & extract of certain sequences
        >>> Sequence.get_split_commands_sequential(True, './input.gz',
'./output.gz', start_sequence=0, sequence_count=10)
        ['zcat "./input.gz" | ( tail -n +1 2> /dev/null) | head -40 | gzip
-c > "./output.gz"']
        >>> Sequence.get_split_commands_sequential(False, './input.fastq',
'./output.fastq', start_sequence=10, sequence_count=10)
        ['tail -n +41 "./input.fastq" 2> /dev/null | head -40 >
"./output.fastq"']
        """
        start_line = start_sequence * 4
        line_count = sequence_count * 4
        # TODO: verify that tail can handle 64-bit numbers
        if is_compressed:
            cmd = 'zcat "%s" | ( tail -n +%s 2> /dev/null) | head -%s |
gzip -c' % (input_name, start_line+1, line_count)
        else:
            cmd = 'tail -n +%s "%s" 2> /dev/null | head -%s'  %
(start_line+1, input_name, line_count)
        cmd += ' > "%s"' % output_name

        return [cmd]
    get_split_commands_sequential =
staticmethod(get_split_commands_sequential)

Best regards

On 25 February 2015 at 15:38, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> On Wed, Feb 25, 2015 at 2:07 PM, Roberto Alonso CIPF <ralo...@cipf.es>
> wrote:
> > 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
>
> Well done :)
>
> It looks like the SAM merge needs fixing then,
>
> $ man egrep
> ...
>        -h, --no-filename
>               Suppress  the  prefixing  of  file  names  on  output.
> This is the default when there is only one file (or only standard
> input) to
>               search.
>
> I filed a pull request adding the -h option to egrep, crediting you:
> https://github.com/galaxyproject/galaxy/pull/4
>
> 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
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