From 26a8718319d59c7ca064445d57ed31fb2f9990bd Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 20 Jul 2020 10:52:50 +0200
Subject: [PATCH] docker: add kallistobustools:0.39.3 with t2g.py
---
.../kallistobustools/0.39.3/Dockerfile | 31 +++++++++++++++++++
.../kallistobustools/0.39.3/docker_init.sh | 4 +++
2 files changed, 35 insertions(+)
create mode 100644 src/.docker_modules/kallistobustools/0.39.3/Dockerfile
create mode 100755 src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
diff --git a/src/.docker_modules/kallistobustools/0.39.3/Dockerfile b/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
new file mode 100644
index 00000000..c993e745
--- /dev/null
+++ b/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
@@ -0,0 +1,31 @@
+FROM python:3.8-alpine
+MAINTAINER Laurent Modolo
+
+ENV B_VERSION=0.39.3
+ENV K_VERSION=0.46.1
+
+RUN apk add --update --no-cache bash musl-dev linux-headers g++ cmake make build-base hdf5 hdf5-dev zlib-dev autoconf && \
+wget https://github.com/BUStools/bustools/archive/v${B_VERSION}.tar.gz && \
+tar xvf v${B_VERSION}.tar.gz && \
+cd bustools-${B_VERSION} && \
+mkdir build && \
+cd build && \
+cmake .. && \
+sed -i -e 's/"Common\.hpp"/"Common\.hpp"\n#include <cmath>/g' ../src/bustools_whitelist.h && \
+sed -i 's/pow/std::pow/g' ../src/bustools_whitelist.cpp && \
+make && \
+make install && \
+wget https://github.com/pachterlab/kallisto/archive/v${K_VERSION}.tar.gz && \
+tar xvf v${K_VERSION}.tar.gz && \
+cd kallisto-${K_VERSION} && \
+mkdir build && \
+cd build && \
+cmake .. && \
+make && \
+make install && \
+wget https://github.com/BUStools/getting_started/releases/download/getting_started/t2g.py && \
+chmod +x t2g.py && \
+mv t2g.py /usr/local/bin/ && \
+rm -R kallisto* bustools* v${K_VERSION}.tar.gz v${B_VERSION}.tar.gz
+
+CMD ["sh"]
diff --git a/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh b/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
new file mode 100755
index 00000000..5cdd8c44
--- /dev/null
+++ b/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/kallistobustools:0.39.3
+docker build src/.docker_modules/kallistobustools/0.39.3 -t 'lbmc/kallistobustools:0.39.3'
+docker push lbmc/kallistobustools:0.39.3
--
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