Hi,
I have my own image registration tool that I've created on my own local
instance of galaxy.
The method takes in two images (*.nii.gz) formats and registers them together,
and produces one registered *.nii.gz file and a *.trsf matrix file.
The first issue encountered was the method was expecting *.nii.gz files as
inputs but was receiving *.dat files. I navigated around this problem as shown
by the files below:
- <<tool id="RegisterAliBabaAffine" name="RegisterAffine">
< <description>two images</description>
< <command
interpreter="bash">$__root_dir__/tools/registration/reg-wrapper.sh $moving
$fixed $outputTRSF $outputImage</command>
- < <inputs>
< <param format="binary" name="moving" type="data" label="Moving Image" />
< <param format="binary" name="fixed" type="data" label="Fixed Image" />
< <param type="hidden" name="outputTRSF" value="output.trsf" label="trsf
file" help="Output File must have .trsf extension" />
< <param type="hidden" name="outputImage" value="output.nii.gz"
label="Image output file" help="Output Image File must have .nii.gz extension"
/>
</inputs>
- < <outputs>
< <data format="input" name="output_TRSF" from_work_dir="output.trsf" />
< <data format="input" name="output_Image" from_work_dir="output.nii.gz" />
</outputs>
< <help>This tool uses Affine Registration to register two images.</help>
</tool>
#!/bin/bash
MOVING=`mktemp --suffix .nii.gz`
FIXED=`mktemp --suffix .nii.gz`
cat $1 > $MOVING
cat $2 > $FIXED
/usr/local/MILXView.12.08.1/BashScripts/RegisterAliBabaAffine -m $MOVING -f
$FIXED -t $3 -o $4
RC=$?
if [[ $RC == 0 ]]; then
OUTPUTTRSF=`mktemp --suffix .trsf`
OUTPUTIMG=`mktemp --suffix .nii.gz`
cat $OUTPUTTRSF > $3
cat $OUTPUTIMG > $4
rm $OUTPUTTRSF
rm $OUTPUTIMG
fi
rm $MOVING
rm $FIXED
exit $RC
This allows them to pass the *.nii.gz files that the registration method is
expecting.
Everything works fine and I can see output generated in the job_working_dir and
the history turns green...
galaxy@bmladmin-OptiPlex-745:~$ ls -lrt
~/galaxy-dist/database/job_working_directory/000/27/
total 2940
-rw------- 1 galaxy nogroup 0 Sep 13 10:15 tmpRfHsOP_stderr
-rw-r--r-- 1 galaxy nogroup 241 Sep 13 10:35 output.trsf
-rw------- 1 galaxy nogroup 80 Sep 13 10:35 tmplmK0V2_stdout
-rw-r--r-- 1 galaxy nogroup 2998272 Sep 13 10:38 output.nii.gz
However, the problem occurs when the files are copied from
~/galaxy-dist/database/job_working_directory/000/27/ to
~/galaxy-dist/database/files/000/. When this happens the files become size = 0.
Any ideas?
-rw-r--r-- 1 galaxy nogroup 0 Sep 13 09:36
/home/galaxy/galaxy-dist/database/files/000/dataset_40.dat
-rw-r--r-- 1 galaxy nogroup 0 Sep 13 09:36
/home/galaxy/galaxy-dist/database/files/000/dataset_41.dat
-rw-r--r-- 1 galaxy nogroup 0 Sep 13 10:38
/home/galaxy/galaxy-dist/database/files/000/dataset_43.dat
-rw-r--r-- 1 galaxy nogroup 0 Sep 13 10:38
/home/galaxy/galaxy-dist/database/files/000/dataset_42.dat
The output in galaxy.log indicates it is successful:
/home/galaxy/galaxy-dist/tools/registration/reg-wrapper.sh
/home/galaxy/galaxy-dist/database/files/000/dataset_23.dat
/home/galaxy/galaxy-dist/database/files/000/dataset_20.dat output.trsf
output.nii.gz galaxy.jobs DEBUG 2012-09-13 10:38:10,334 The tool did not define
exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG
2012-09-13 10:38:10,361 finish(): Moved
/home/galaxy/galaxy-dist/database/job_working_directory/000/27/output.trsf to
/home/galaxy/galaxy-dist/database/files/000/dataset_42.dat as directed by
from_work_dir galaxy.jobs DEBUG 2012-09-13 10:38:10,380 finish(): Moved
/home/galaxy/galaxy-dist/database/job_working_directory/000/27/output.nii.gz to
/home/galaxy/galaxy-dist/database/files/000/dataset_43.dat as directed by
from_work_dir galaxy.jobs DEBUG 2012-09-13 10:38:10,609 job 27 ended
Is the issue copying *.nii.gz files and *.trsf file into *.dat files? Anyway
around this?
I've also modified ~/galaxy-dist/lib/galaxy/jobs/__init__.py (line 363) to
change shutil.move
To shutil.copy2 (same results)
Also put in a different output path to copy to. But essentially we have files
with size in ~/galaxy-dist/database/job_working_directory/000/id/, but they
files are size 0 after the move into ~/galaxy-dist/database/files/000
Thanks
Neil
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