I am trying to map a a fastqsacer file and map it with bwa, my bwa tool config file is this:
<tool id="bwa_mio" name="map with bwa">
<description>map with bwa</description>
<parallelism method="basic" split_size="2" split_mode="number_of_parts"></parallelism>
<command>
bwa mem /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa $input > $output 2>xx</command>
<inputs>
<param format="fastqsanger" name="input" type="data" label="fastq"/>
</inputs>
<outputs>
<data format="sam" name="output" />
</outputs>
<help>
bwa
</help>
</tool>
And when I see the stderr I see this error:
type object 'Sequence' has no attribute 'get_split_commands_sequential'
It seems that this command that I see in the log is not working
galaxy.jobs.runners DEBUG 2015-02-11 16:33:48,738 (74) command is: /home/ralonso/galaxy-dist/extract_dataset_parts.sh /home/ralonso/galaxy-dist/database/job_working_directory/000/74/task_0; bwa mem /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa /home/ralonso/galaxy-dist/database/job_working_directory/000/74/task_0/dataset_8.dat > /home/ralonso/galaxy-dist/database/job_working_directory/000/74/task_0/dataset_75.dat
When I go directly to the code, around line 559 of class galaxy.datatypes.sequence I can't find this function get_split_commands_sequential anywhere.
Any idea?
Thank you very much
Regards
--
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)