-
Notifications
You must be signed in to change notification settings - Fork 21
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
added tracy singularity definition file
- Loading branch information
1 parent
e52e17c
commit 629e60a
Showing
2 changed files
with
51 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,7 @@ | ||
You can build a [tracy](https://github.com/gear-genomics/tracy) singularity container (SIF file) using | ||
|
||
`sudo singularity build tracy.sif tracy.def` | ||
|
||
Once you have built the container you can run analysis using | ||
|
||
`singularity exec tracy.sif tracy basecall input.ab1` |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,44 @@ | ||
# Build image | ||
BootStrap: library | ||
From: ubuntu:16.04 | ||
Stage: build | ||
|
||
%post | ||
apt-get -y update | ||
apt-get install -y build-essential cmake g++ gfortran git hdf5-tools libboost-date-time-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-iostreams-dev libbz2-dev libhdf5-dev libncurses-dev liblzma-dev zlib1g-dev | ||
apt-get clean | ||
rm -rf /var/lib/apt/lists/* | ||
cd /opt | ||
git clone --recursive https://github.com/gear-genomics/tracy.git | ||
cd /opt/tracy/ | ||
make STATIC=1 all | ||
make install | ||
|
||
|
||
# Final image | ||
BootStrap: library | ||
From: alpine:3.9 | ||
Stage: final | ||
|
||
%files from build | ||
/opt/tracy/bin/tracy /bin/tracy | ||
|
||
%post | ||
TRACYVERSION=`./bin/tracy --version` | ||
echo "export TRACYVERSION=\"${TRACYVERSION}\"" >> $SINGULARITY_ENVIRONMENT | ||
CREATEDATE=`date` | ||
echo "export CREATEDATE=\"${CREATEDATE}\"" >> $SINGULARITY_ENVIRONMENT | ||
|
||
%environment | ||
export PATH=/bin:$PATH | ||
|
||
%runscript | ||
tracy | ||
|
||
%labels | ||
Singularity definition file version v0.0.1 | ||
|
||
%help | ||
This is a container running tracy. | ||
You can run tracy on files inside the directory where you start | ||
the container, i.e.: singularity exec tracy.sif tracy basecall input.ab1 |