Hello,
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)
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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
