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Question: MACS2 callpeak : MACS2_model.r not found
0
gravatar for plindenbaum
2.7 years ago by
plindenbaum • 90
France
plindenbaum • 90 wrote:

Hi all, I'm trying to use MACS2 on galaxy. It was installed on our local instance via the toolshed.

When "MACS2 callpeak" is invoked, there's a call to Rscript

## run R to create pdf from model script
#if $nomodel_type.nomodel_type_selector == 'create_model' and 'pdf' in str($outputs).split(','):
    &&
    Rscript MACS2_model.r > MACS2_model.r.log
#end if

But I get an error from Galaxy because there is no file MACS2_model.r anywhere (find / -type f -name "MACS2_model.r")

Any idea ?

thanks.
rscript macs2 • 1.2k views
ADD COMMENT • link •
modified 2.7 years ago by Bjoern Gruening ♦ 5.1k • written 2.7 years ago by plindenbaum • 90

ok, as far as I can see xxx_model.r is created by MACS2... https://github.com/taoliu/MACS/blob/a3438e855d0e2824091168f03ee8586d59dbc5ae/DEBIAN/macs.man#L243

ADD REPLY • link written 2.7 years ago by plindenbaum • 90
2
gravatar for Bjoern Gruening
2.7 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

if I'm not mistaken this script is generated by MACS2 during runtime.

Ciao, Bjoern
ADD COMMENT • link written 2.7 years ago by Bjoern Gruening ♦ 5.1k

Agree. For the problem, perhaps compare the R dependency you are using vs the repo requirements? You might consider reinstalling with managed dependencies to pull the version of R the tool is expecting. - Jen, Galaxy team

ADD REPLY • link written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k
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