updated dv dockers with correct git commits (#54)

* overhauled deepvariant and fq2sortedbam; main targets run files, docker file; next need test and remove unnecessary files

* error fixed in fq2sortedbams

* fixed error in deepvar py and docker files

* issues fixed to get the running docker based pipelines

* fixed fq2sortedbam

* update install.sh

* update install.sh

* fix calling the python main script from run python script with args as a param

* updated fq2bma docker and deep dockers

* minor fix to fq2bam

* minor fix in install.sh

* minor fixes

* updated docker and runfile

* updates

* dockers

* udpated HWconfigure

* udpated HWconfigure

* udpated HWconfigure

* updates

* dv1 done

* updates

* updates

* updated bams2vcf

* updates

* updates

* added numactl in bams2vcf docker

* final touches to fq2bam, added doc.txt file

* some verification, few tests can be done by engineers

* added docs

* cleanup

* added STAT and bwa-meth

* updated install.sh with star and bwa-meth

* fixed install.sh

* fixes to install.sh

* bwa-meth and star added, star is slow on comms, need to figure it out. tested meth as well works fine on small dataset; I will generate large dataset for testing/benchmarking using Sherman. Doing Sherman runs on tiergaten due to large runtime.

* readme

* moved env file

* fixed params

* updated the readme

* README

* updated the dockers

* added git clone commits

---------

Co-authored-by: Ubuntu <[email protected]>
Co-authored-by: vasimuddin.md <[email protected]>
Co-authored-by: vasimuddin.md <[email protected]>
Co-authored-by: vasimuddin.md <[email protected]>
Co-authored-by: vasimuddin.md <[email protected]>
Co-authored-by: vasimuddin.md <[email protected]>
Co-authored-by: Ubuntu <[email protected]>
Co-authored-by: manasi-t24 <[email protected]>

Author: 9 people

pipelines/deepvariant-based-germline-variant-calling-fq2vcf/Dockerfile_bams2vcf

@@ -50,6 +50,8 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-ins
 WORKDIR /opt
 
 RUN git clone --recursive https://github.com/IntelLabs/open-omics-deepvariant.git
+RUN git checkout bdcc819
+
 RUN cp -r ./open-omics-deepvariant /opt/deepvariant/
 #COPY ./open-omics-deepvariant /opt/deepvariant/
 #RUN cp -r /opt/deeptrio /opt/deepvariant/
@@ -58,7 +60,9 @@ RUN rm -rf open-omics-deepvariant
 
 
 RUN git clone --recursive https://github.com/samtools/bcftools.git
+RUN git checkout e4a21b8
 RUN git clone --recursive https://github.com/samtools/htslib.git
+RUN git checkout 3668b932bdb9f737c4af9c28ddbf0472156a5f24
 
 
 WORKDIR /opt/deepvariant
@@ -247,6 +251,9 @@ RUN apt-get -y update && \
 WORKDIR /
 #COPY extra_scripts .
 RUN git clone --recursive https://github.com/IntelLabs/Open-Omics-Acceleration-Framework.git
+
+RUN git checkout 060a0c76ad4ded6d6de709b0466b8bdafdc6053d
+
 WORKDIR /Open-Omics-Acceleration-Framework/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/
 
 RUN apt-get update

pipelines/deepvariant-based-germline-variant-calling-fq2vcf/Dockerfile_fq2bams

@@ -6,7 +6,7 @@ FROM ${BASE_IMAGE} as conda_setup
 
 WORKDIR /
 RUN git clone --recursive https://github.com/IntelLabs/Open-Omics-Acceleration-Framework.git
-
+RUN git checkout 060a0c76ad4ded6d6de709b0466b8bdafdc6053d
 WORKDIR /Open-Omics-Acceleration-Framework/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/
 
 RUN conda env create --name dv_env -f environment.yml
@@ -31,6 +31,7 @@ RUN source ~/.bashrc
 
 WORKDIR /
 RUN git clone --recursive https://github.com/IntelLabs/Open-Omics-Acceleration-Framework.git
+RUN git checkout 060a0c76ad4ded6d6de709b0466b8bdafdc6053d
 
 WORKDIR /Open-Omics-Acceleration-Framework/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/