From 8e441189bfc1363c1614167d7ee24241ba2f33d3 Mon Sep 17 00:00:00 2001 From: AbhishekGogna Date: Thu, 17 Mar 2022 13:39:40 +0100 Subject: [PATCH 1/7] first commit for a bio_ana container --- Singularity-bio_ana.def | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 Singularity-bio_ana.def diff --git a/Singularity-bio_ana.def b/Singularity-bio_ana.def new file mode 100644 index 0000000..172e3c7 --- /dev/null +++ b/Singularity-bio_ana.def @@ -0,0 +1,23 @@ +# builds on top of singularty rstudio +# done: add vcftools +# todo: add flexibility to choose python version. +# todo: add jupyterlab and anaconda. +# todo: add other essentials for basic biological studies viz. galaxy, GATK and more + +BootStrap: localimage +From: rstudio.sif + +%labels + Maintainer Abhi + RStudio_Version 1.4.1717 # from base image +%help +# Hope/to check - for the base image packages, help section will be carried forward. +%post + git clone https://github.com/vcftools/vcftools.git + cd vcftools + ./autogen.sh + ./configure + make + make install +%apprun vcftools + exec vcftools "${@}" From 78352b532a2b2bd77d3e25131e904ba991bd7f2b Mon Sep 17 00:00:00 2001 From: AbhishekGogna Date: Thu, 17 Mar 2022 13:46:00 +0100 Subject: [PATCH 2/7] first commit for a bio_ana container --- Singularity-bio_ana | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 Singularity-bio_ana diff --git a/Singularity-bio_ana b/Singularity-bio_ana new file mode 100644 index 0000000..172e3c7 --- /dev/null +++ b/Singularity-bio_ana @@ -0,0 +1,23 @@ +# builds on top of singularty rstudio +# done: add vcftools +# todo: add flexibility to choose python version. +# todo: add jupyterlab and anaconda. +# todo: add other essentials for basic biological studies viz. galaxy, GATK and more + +BootStrap: localimage +From: rstudio.sif + +%labels + Maintainer Abhi + RStudio_Version 1.4.1717 # from base image +%help +# Hope/to check - for the base image packages, help section will be carried forward. +%post + git clone https://github.com/vcftools/vcftools.git + cd vcftools + ./autogen.sh + ./configure + make + make install +%apprun vcftools + exec vcftools "${@}" From bbbbafae2c2ebd47760f23ee0fb5376ff30bd317 Mon Sep 17 00:00:00 2001 From: abhi_g <66737333+AbhishekGogna@users.noreply.github.com> Date: Thu, 17 Mar 2022 13:46:38 +0100 Subject: [PATCH 3/7] Delete Singularity-bio_ana.def --- Singularity-bio_ana.def | 23 ----------------------- 1 file changed, 23 deletions(-) delete mode 100644 Singularity-bio_ana.def diff --git a/Singularity-bio_ana.def b/Singularity-bio_ana.def deleted file mode 100644 index 172e3c7..0000000 --- a/Singularity-bio_ana.def +++ /dev/null @@ -1,23 +0,0 @@ -# builds on top of singularty rstudio -# done: add vcftools -# todo: add flexibility to choose python version. -# todo: add jupyterlab and anaconda. -# todo: add other essentials for basic biological studies viz. galaxy, GATK and more - -BootStrap: localimage -From: rstudio.sif - -%labels - Maintainer Abhi - RStudio_Version 1.4.1717 # from base image -%help -# Hope/to check - for the base image packages, help section will be carried forward. -%post - git clone https://github.com/vcftools/vcftools.git - cd vcftools - ./autogen.sh - ./configure - make - make install -%apprun vcftools - exec vcftools "${@}" From 101c940eaf8c44b97ac45db63f26aec18012d341 Mon Sep 17 00:00:00 2001 From: AbhishekGogna Date: Thu, 17 Mar 2022 16:48:22 +0100 Subject: [PATCH 4/7] Added jupyter lab --- Singularity-bio_ana | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/Singularity-bio_ana b/Singularity-bio_ana index 172e3c7..e5ce651 100644 --- a/Singularity-bio_ana +++ b/Singularity-bio_ana @@ -1,7 +1,7 @@ # builds on top of singularty rstudio # done: add vcftools +# done: add jupyterlab # todo: add flexibility to choose python version. -# todo: add jupyterlab and anaconda. # todo: add other essentials for basic biological studies viz. galaxy, GATK and more BootStrap: localimage @@ -13,11 +13,17 @@ From: rstudio.sif %help # Hope/to check - for the base image packages, help section will be carried forward. %post + #vcftools git clone https://github.com/vcftools/vcftools.git cd vcftools ./autogen.sh ./configure make make install + + #jupyter-lab + pip install jupyterlab + #todo: something to stat this with ./rstudio prompt! + %apprun vcftools exec vcftools "${@}" From 5202c3756006b5a1c12adbf780b76e17bfb41311 Mon Sep 17 00:00:00 2001 From: AbhishekGogna Date: Thu, 17 Mar 2022 16:51:07 +0100 Subject: [PATCH 5/7] typo corrected --- Singularity-bio_ana | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Singularity-bio_ana b/Singularity-bio_ana index e5ce651..1d8b75b 100644 --- a/Singularity-bio_ana +++ b/Singularity-bio_ana @@ -27,3 +27,5 @@ From: rstudio.sif %apprun vcftools exec vcftools "${@}" +%apprun jupyter-lab + exec jupyter-lab "${@}" From dd8e441f41742ce6545309875f223a933f1a7687 Mon Sep 17 00:00:00 2001 From: AbhishekGogna Date: Fri, 25 Mar 2022 16:06:14 +0100 Subject: [PATCH 6/7] added more tools --- Singularity-bio_ana | 47 +++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 43 insertions(+), 4 deletions(-) diff --git a/Singularity-bio_ana b/Singularity-bio_ana index 1d8b75b..6d635a1 100644 --- a/Singularity-bio_ana +++ b/Singularity-bio_ana @@ -13,18 +13,57 @@ From: rstudio.sif %help # Hope/to check - for the base image packages, help section will be carried forward. %post + #jupyter-lab + pip install jupyterlab + + #make directory for downloading temporary files + mkdir tmp_download + cd tmp_download + #vcftools git clone https://github.com/vcftools/vcftools.git - cd vcftools + mv vcftools /opt + cd /opt/vcftools ./autogen.sh ./configure make make install + cd /tmp_download - #jupyter-lab - pip install jupyterlab + #blast + wget https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.13.0+-x64-linux.tar.gz + tar zxvpf ncbi-blast-2.13.0+-x64-linux.tar.gz + mv ncbi-blast-2.13.0+ /opt/blast + mkdir /opt/blast/blastdb #todo: something to stat this with ./rstudio prompt! - + + #samtools, bcftools and hstlib + wget https://github.com/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2 + wget https://github.com/samtools/bcftools/releases/download/1.15/bcftools-1.15.tar.bz2 + wget https://github.com/samtools/htslib/releases/download/1.15/htslib-1.15.tar.bz2 + + for f in samtools-1.15 bcftools-1.15 htslib-1.15 + do + tar -xvf "$f.tar.bz2" + cd "$f" + ./configure --prefix="/opt/$f" + make + make install + echo "done istalling $f" + cd .. + done + + # clean the downloads + rm -rf /tmp_download + +%environment + export PATH=/opt/blast/bin:${PATH} + export BLASTDB=/opt/blast/blastdb + export PATH=/opt/samtools-1.15/bin:${PATH} + export PATH=/opt/bcftools-1.15/bin:${PATH} + export PATH=/opt/hstlib-1.15/bin:${PATH} + #open rstudio and add these lines to .bshrc file in the /proj folder + %apprun vcftools exec vcftools "${@}" %apprun jupyter-lab From 1864fe82b823cf7f41e757f00ea5a02d9e7cd2ac Mon Sep 17 00:00:00 2001 From: AbhishekGogna Date: Fri, 25 Mar 2022 16:31:05 +0100 Subject: [PATCH 7/7] added more tools --- Singularity-bio_ana | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/Singularity-bio_ana b/Singularity-bio_ana index 6d635a1..849053d 100644 --- a/Singularity-bio_ana +++ b/Singularity-bio_ana @@ -1,6 +1,7 @@ # builds on top of singularty rstudio # done: add vcftools # done: add jupyterlab +# done: add samtools package, blast # todo: add flexibility to choose python version. # todo: add other essentials for basic biological studies viz. galaxy, GATK and more @@ -63,8 +64,3 @@ From: rstudio.sif export PATH=/opt/bcftools-1.15/bin:${PATH} export PATH=/opt/hstlib-1.15/bin:${PATH} #open rstudio and add these lines to .bshrc file in the /proj folder - -%apprun vcftools - exec vcftools "${@}" -%apprun jupyter-lab - exec jupyter-lab "${@}"