stix-docker

Dockerfile for Ryan Layer's stix sv annotator + associated tools

About

This is my first docker image.

Uploaded to the hub here: https://hub.docker.com/repository/docker/philliparichmond/stix-sv/general

I had trouble installing giggle + stix (libcurl hatred in shared HPC with make-based install).

Tools in this image:

Samtools: https://github.com/samtools/samtools
STIX: https://github.com/ryanlayer/stix
excord: https://github.com/brentp/excord
giggle: https://github.com/ryanlayer/giggle

I made this with motivation and starting point here: https://github.com/apaul7/docker-stix

Building

Making the image from the command line with docker installed on my mac:

docker build -t philliparichmond/stix-sv:20220421 /some/path/to/this/repo/stix-docker/

I then added it to docker hub with this:

docker push philliparichmond/stix-sv:20220421

Pulling + usage

You can pull the image from the Public docker repo:

docker pull docker://philliparichmond/stix-sv:20220421

Testing + usage

Testing that it works and some usage pieces:
Samtools

docker run -i philliparichmond/stix-sv:20220421 samtools

Stix

docker run -i philliparichmond/stix-sv:20220421 stix

Giggle

docker run -i philliparichmond/stix-sv:20220421 giggle

excord

docker run -i philliparichmond/stix-sv:20220421 excord

With Singularity

Singularity pull docker image

singularity pull  docker://philliparichmond/stix-sv:20220421

Singularity run docker image

singularity exec -i stix-sv_20220421.sif samtools

singularity exec -i stix-sv_20220421.sif stix

singularity exec -i stix-sv_20220421.sif giggle

singularity exec -i stix-sv_20220421.sif excord

Example usage of these tools with 1kG_Trio data

Make Giggle Index from Excord Output

I have these files in a directory called Excord_Output

Excord_Output/HG00403.bed.gz
Excord_Output/HG00404.bed.gz
...

For ~1500 samples.

I create a giggle index like this using a docker for Stix+giggle+excord+samtools, which you can get here: https://hub.docker.com/repository/docker/philliparichmond/stix-sv/general

Stix_SIF=/mnt/common/Precision/STIX/stix.sif

WorkingDir=/mnt/common/OPEN_DATA/1kG_Trio/
DataDir=$WorkingDir/Excord_Output/
IndexDir=${WorkingDir}STIX_Index
rm -rf $IndexDir
mkdir -p $IndexDir

# Make a giggle index bash script. This is necessary because singularity won't evaluate the blob format of $IndexDir/*gz
IndexScript=$WorkingDir/IndexGiggle.sh
# clean up if it exists already
rm $IndexScript

# here I'm making this giggle script that will be passed to singularity below
# Have to do this because singularity can't evaluate glob format for *.bed.gz
# Thank Brentp for that help on smoove.

echo cd $DataDir > $IndexScript
echo giggle index -s -f -o "$IndexDir" -i "*.bed.gz" >> $IndexScript

# Run giggle index
singularity exec \
	-B $WorkingDir \
	-B $IndexDir \
	-B $DataDir \
	$GiggleSIF \
	bash $IndexScript

The index command looks like this:

giggle index -s -f -o /mnt/common/OPEN_DATA/1kG_Trio/STIX_Index -i /mnt/common/OPEN_DATA/1kG_Trio//Excord_Output/*.bed.gz

Now this gives me a nice large directory with a bunch of .dat and .idx files. Unclear if it's correct, ran for ~5 min and exits with no errors.

STIX_Index/

Make PED file with sample name and sample .bed.gz file

Next step is I want to make a PED file containing the sample + filenames. I do that with a little bash script working on the input directory for excord files. Bash script looks like:

# This script takes in a directory of excord .bed.gz files, and makes a single file with format:
# sampleID      Filename.Bed.gz

# I'll do that with this code:
shopt -s nullglob
DataDir=/mnt/common/OPEN_DATA/1kG_Trio/Excord_Output/
Files=($DataDir/*.bed.gz)

pedfile=$DataDir/AllSamples.ped
# Delete if it exists
rm $pedfile
# give it a header
echo "Sample    Sex     Alt_File" > $pedfile

for file in ${Files[@]};
do
        basefile=$(basename -- "$file")
        sampleID="${basefile%%.*}"
        echo $sampleID  $file   
        echo "$sampleID  $file" >> $pedfile     
done

That gives me a ped file that looks like this:

Sample	Alt_File
HG00403 /mnt/common/OPEN_DATA/1kG_Trio/Excord_Output//HG00403.bed.gz
HG00404 /mnt/common/OPEN_DATA/1kG_Trio/Excord_Output//HG00404.bed.gz
HG00405 /mnt/common/OPEN_DATA/1kG_Trio/Excord_Output//HG00405.bed.gz
...

Make STIX database from giggle indexed output

Now back to STIX to make the database given the index directory, and the ped file.

Stix_SIF=/mnt/common/Precision/STIX/stix.sif

WorkingDir=/mnt/common/OPEN_DATA/1kG_Trio/
DataDir=$WorkingDir/Excord_Output/
SVDir=$WorkingDir/MantaSmoove/
IndexDir=$WorkingDir/STIX_Index/
PedFile=$DataDir/AllSamples.ped

# Initialize stix database with giggle index and bed files
singularity exec \
        -B $WorkingDir \
        -B $IndexDir \
        -B $DataDir \
        $Stix_SIF \
        stix \
        -i $IndexDir \
        -p $PedFile \
        -d $DataDir/AllSamples.stix.db \
        -c 2

And I get an error:

stix: ERROR ped_create_db(): PED file /mnt/common/OPEN_DATA/1kG_Trio/Excord_Output//HG00403.bed.gz not found in giggle index.

I have tried rerunning with different ped file columns too, and with only the base name in the created ped file, e.g. modified from above:

for file in ${Files[@]};
do
        basefile=$(basename -- "$file")
        sampleID="${basefile%%.*}"
        echo $sampleID  $basefile   
        echo "$sampleID  $basefile" >> $pedfile     
done

But still get error:

stix: ERROR ped_create_db(): PED file HG00404.bed.gz not found in giggle index.

Now I'm thinking that the giggle index is actually incomplete. When it ran, it only output that it had processed the number of lines for HG00403.bed.gz:

Indexed 14992289 intervals.

Rerunning the giggle index, perhaps it's a matter of the placement of " in the bash script. It now looks like this:

giggle index -s -f -o /mnt/common/OPEN_DATA/1kG_Trio/STIX_Index -i "/mnt/common/OPEN_DATA/1kG_Trio//Excord_Output/*.bed.gz"

We'll see if that works....

Phillip-a-richmond/stix-docker