new /ls2 script location

Dockerfile

@@ -1,32 +1,41 @@
-FROM fredhutch/ls2_easybuild_foss:2016b
+FROM fredhutch/ls2_easybuild_toolchain:foss-2016b
+
+# Remember the default use is LS2_USERNAME, not root
+
+# DEPLOY_PREFIX comes from ls2_lmod container, two containers up!
+
+# easyconfig to build - leave '.eb' off
+ARG EB_NAME
+ENV EB_NAME=${EB_NAME}
+
+# libibverbs required for foss toolchains
+ENV INSTALL_OS_PKGS ""
 
-# easyconfig to build 
-ENV EASYCONFIG_NAME my_best_easyconfig.eb
-# required OS packages for the build
-ENV INSTALL_OS_PKGS "awscli build-essential pkg-config libssl-dev unzip libc6-dev"
 # os pkg list to be removed after the build - in EasyBuild, the 'dummy' toolchain requires build-essential
 # also, the current toolchain we are using (foss-2016b) does not actually include 'make'
 # removing build-essential will mean the resulting container cannot build additional software
-ENV UNINSTALL_OS_PKGS "build-essential"
-# switch to our non-root user
-USER neo
-# copy in AWS Batch's "fetch-and-run" for S3-based scripts
-COPY aws-batch-helpers/fetch-and-run/fetch_and_run.sh /home/neo/fetch_and_run.sh
-# copy in easyconfigs (so many due to missing dependencies in existing easyconfigs)
-COPY easyconfigs/* /app/fh_easyconfigs/
-# R sources that cannot be programmatically downloaded
-COPY sources/* /app/sources/
-# run script to download larger sources
-RUN /bin/bash /app/sources/download_sources.sh
-# install build-essential, build R, remove build-essential
-# EVERYTHING beyond build-essential needs to be moved into EB!!!
+ENV UNINSTALL_OS_PKGS ""
+
+# copy install and deploy scripts in
+COPY install.sh /ls2/
+COPY deploy.sh /ls2/
+
+# install and uninstall build-essential in one step to reduce layer size
+# while installing Lmod, again must be root
 USER root
-RUN apt-get update -y && apt-get install -y $INSTALL_OS_PKGS && \
-    su -c ". /app/lmod/lmod/init/bash && \
-           module use /app/modules/all && \
-           module load EasyBuild && \
-           eb -l $EASYCONFIG_NAME --robot" - neo && \
-    apt-get remove -y --purge $UNINSTALL_OS_PKGS && \
-    apt-get autoremove -y
-USER neo
+RUN DEBIAN_FRONTEND=noninteractive \
+    apt-get update -y \
+    && apt-get install -y ${INSTALL_OS_PKGS} \
+    && su -c "/bin/bash /ls2/install.sh" ${LS2_USERNAME} \
+    && AUTO_ADDED_PKGS=$(apt-mark showauto) apt-get remove -y --purge ${UNINSTALL_OS_PKGS} ${AUTO_ADDED_PKGS} \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/*
+
+# gather installed pkgs list
+RUN dpkg -l > /ls2/installed_pkgs.${EB_NAME}
+
+# switch to LS2 user for future actions
+USER ${LS2_USERNAME}
+WORKDIR /home/${LS2_USERNAME}
+SHELL ["/bin/bash", "-c"]
 

deploy.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+# required env vars: OUT_UID, OUT_GID, DEPLOY_PREFIX
+
+set -x
+set -e
+
+groupadd -g $OUT_GID outside_group
+useradd -u $OUT_UID -g outside_group outside_user 
+
+apt-get update -y
+apt-get install -y build-essential
+
+su -c "/bin/bash /ls2/install.sh" outside_user
+
+su -c "source ${DEPLOY_PREFIX}/lmod/lmod/init/bash \
+       && ${DEPLOY_PREFIX}/lmod/lmod/libexec/update_lmod_system_cache_files ${DEPLOY_PREFIX}/modules/all" outside_user
+
+AUTO_ADDED_PKGS=$(apt-mark showauto) apt-get remove -y --purge build-essential ${AUTO_ADDED_PKGS}
+apt-get autoremove -y
+rm -rf /var/lib/apt/lists/*

install.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+set -x
+set -e
+
+# variables used: TOOLCHAIN, DEPLOY_PREFIX
+
+# try to preserve group write here
+umask 002
+
+# load modules
+source ${DEPLOY_PREFIX}/lmod/lmod/init/bash
+module use ${DEPLOY_PREFIX}/modules/all
+
+# load Easybuild
+module load EasyBuild
+
+# build the easyconfig file
+eb -l ${TOOLCHAIN}.eb --robot
+

sources/download_sources.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
 # script to download sources too large to fit into a git repo
-curl -o /app/sources/jdk-8u92-linux-x64.tar.gz https://s3-us-west-2.amazonaws.com/ls2-sources/jdk-8u92-linux-x64.tar.gz
+#curl -o /app/sources/jdk-8u92-linux-x64.tar.gz https://s3-us-west-2.amazonaws.com/ls2-sources/jdk-8u92-linux-x64.tar.gz