Public Repository

Last pushed: 2 years ago
Short Description
This is docker image that runs several SBML tools developed at The University of South Dakota.
Full Description

usdbioinformatics/sbmldock

This is docker image that runs several SBML tools developed at The
University of South Dakota.

Info

The are several tools you can run from command line using this docker
image. Check the Tools section for information on each tool in the
list and commands to run them. We are also providing some test data
to run them on, but you can use your own data as well.

Tools List


1. ParaABioS
2. SBMLChecker
3. SBMLCompare
4. SBMLMerge
5. SBMLSplit
6. SBMLModeler
7. SBMLAnnotate

Tools

There is test data for each tool and you also want to map folders into your
running docker images so you can get the output back from the tools.
This is done by using -v /host/folder:/container/folder and we will
also tell it to run in the container's folder so that when the run is
over all your output files come back out for you to look at. We will
do that with -w /container/folder noting it's the same place we are
mounting into. See examples below for this in practice. Another thing
to be aware of is that files will be owned by root when they come back
out of the container. So you may need root privileges to work with
the output files.

ParaABioS


There is test data in the /opt/ParaABioS/ folder to test the tool on. To
execute ParaABioS you want to do ParaABioS <inputfile1> <inputfile2> <distance> <ratio>.
Given the image is named usdbioinformatics/sbmldock and you have a folder to mount
in the image at /home/wjconn/SBMLDock/mount then you would use a
command line like this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock ParaABioS /opt/ParaABioS/file1.txt /opt/ParaABioS/file2.txt 6 0.7

If you have your own files you wish to run the tool on, make sure to place
the files in the folder you mount inside the container. For me this
would be inside the /home/wjconn/SBMLDock/mount folder. It's the
same place your output files show up when the container is done
running. That command line would look like this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock ParaABioS file1.txt file2.txt 6 0.7

SBMLChecker


There is test data in the /opt/SBMLChecker/ folder to test the tool with. To
execute SBMLChecker you want to use SBMLChecker <inputfile>.
Given the image is named usdbioinformatics/sbmldock and you have a folder to mount
in the image at /home/wjconn/SBMLDock/mount then you would use a
command line like this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLChecker /opt/SBMLChecker/one.xml

There will be information printed to the screen and there will be the error
report output files that show up in your mounted directory. To
use your own file, again, make sure it is in the mount directory
and use a similar command line to this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLChecker one.xml

SBMLCompare


There is test data in the /opt/SBMLCompare/ folder to test the tool with. To
execute SBMLCompare you want to use SBMLCompare <inputfile1> <inputfile2>.
Given the image is named usdbioinformatics/sbmldock and you have a folder to mount
in the image at /home/wjconn/SBMLDock/mount then you would use a
command line like this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLCompare /opt/SBMLCompare/one.xml /opt/SBMLCompare/two.xml

This will print a bunch of text to screen and there will be an excel file
called sbml_compare_report.xls and a xml file called sbml_compare_report.xml
created in the mount folder as output from the tool. To use your own
two files with the tool, make sure they are in the mount directory and
use a similar command line to this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLCompare one.xml two.xml

SBMLMerge


There is test data in the /opt/SBMLMerge/ folder to test the tool with. To
execute SBMLMerge you want to use SBMLMerge <edit distance int[0-10]> <similarity ratio float[0-1]> <inputfile1> <inputfile2> <optional input files up to 6>
Given the image is named usdbioinformatics/sbmldock and you have a folder to mount in
the image at /home/wjconn/SBMLDock/mount then you owuld use a command
line like this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLMerge 6 0.7 /opt/SBMLMerge/one.xml /opt/SBMLMerge/two.xml

This will print a lot of info to the screen and you will get a mergedmodel.xml
file in your mounted directory. To use your own data files, first put
them in the directory your going to mount in the container and then use
a command line similar to this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLMerge 6 0.7 one.xml two.xml

SBMLSplit


There is test data in the /opt/SBMLSplit/ folder to test the tool with. To
execute SBMLSplit you want to use SBMLSplit <flag> <inputfile> where
your flag is C or R to split on Compound or Reaciton and the file
is the file you want to split. Given the image is named usdbioinformatics/sbmldock
and you have a folder to mount in the image at /home/wjconn/SBMLDock/mount
then you would use a command line like this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLSplit C /opt/SBMLSplit/one.xml

This will print out some information to the screen and in your mount folder you
will end up with S0.xml and S1.xml files that are the split files. To
use your own file with the tool, make sure it is in the mount directory
and use a similar command line to this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLSplit C one.xml

SBMLModeler


SBMLModeler pulls data it needs from multiple sources on the internet but you
need to supply the pathway to the program on the command line. For a
list of pathways to use, please check the Pathwayslist.txt file by
using cat /opt/SBMLModeler/Pathwayslist.txt. Assuming your image is
named usdbioinformatics/sbmldock and you have a folder to mount in the image at
/home/wjconn/SBMLDock/mount then you would use a command line like
this to see the pathways:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock cat /opt/SBMLModeler/Pathwayslist.txt

Once you have your pathway picked out you can run SBMLModeler by using SBMLModeler <Path to store file> <Pathway name>.
It's best to simple store the files in the directory we are in so they
come back out of the container into the mount directory. So we will
run it with a command line like this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLModeler . "folate biosynthesis"

SBMLAnnotate


There is test data in the /opt/SBMLAnnotate/ folder to test the tool with. To
execute SBMLAnnotate you want to use SBMLAnnotate <inputfile> <outputfile>.
Given the image is named usdbioinformatics/sbmldock and you have a folder to mount
in the image at /home/wjconn/SBMLDock/mount then you would use a
command line like this:

docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLAnnotate /opt/SBMLAnnotate/one.xml out.xml

This will put the out.xml file in your mount directory after it's finished. To
use your own file with the tool, make sure it is in the mount directory
and use a similar command line to this:

    docker run -v /home/wjconn/SBMLDock/mount:/tmp -w /tmp usdbioinformatics/sbmldock SBMLAnnotate one.xml out.xml

Credits


The University of South Dakota

Docker Pull Command
Owner
usdbioinformatics