MNT: updates to dev and runtime image defs

.docker/bip-dev/create_dev_env.sh

@@ -9,30 +9,27 @@ channels=(-c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/development/
 conda create -y ${channels[@]}   \
       -p ./${envdir}             \
       "python=${PYTHON_VERSION}" \
-      c-compiler                 \
-      cxx-compiler               \
-      pytest                     \
       coverage                   \
-      pytest-cov                 \
+      dmri-amico                 \
+      file-tree                  \
+      file-tree-fsl              \
       fsl-gradunwarp             \
       fsl-avwutils               \
+      fsl-cluster                \
       fsl-pyfix                  \
-      file-tree file-tree-fsl    \
+      fsl-pipe                   \
       fsl_sub                    \
       fsl_sub_plugin_slurm       \
       fsl_sub_plugin_sge         \
-      jinja2
+      jinja2                     \
+      pytest                     \
+      pytest-cov
+
 
 echo "channels:"                                                        > ${envdir}/.condarc
 echo "  https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/development/" >> ${envdir}/.condarc
 echo "  https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/"      >> ${envdir}/.condarc
 echo "  conda-forge"                                                   >> ${envdir}/.condarc
 
-
-source activate ${envdir}
-pip install dmri-amico
-pip install git+https://git.fmrib.ox.ac.uk/fsl/pipe-tree.git
-
-conda remove -p ${envdir} c-compiler cxx-compiler
 conda clean -y -all
 pip cache purge

.docker/bip-image/build_image.sh

@@ -4,12 +4,23 @@ set -e
 
 SHELL_PROFILE=/root/.bashrc
 
-export TAR_OPTIONS=--no-same-owner
-export WGET_OPTIONS=--no-check-certificate
+export TAR_OPTIONS="--no-same-owner"
+export WGET_OPTIONS="--no-check-certificate -q"
 
 # OS / build dependencies
 yum install -y epel-release
-yum install -y openssh-clients git nano wget curl unzip python3 parallel
+yum install -y \
+    curl \
+    freetype \
+    git \
+    mesa-libGL \
+    nano \
+    openssh-clients \
+    parallel \
+    python3 \
+    tcsh \
+    unzip \
+    wget
 
 # FSL
 FSL_URL=https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py
@@ -20,7 +31,11 @@ echo -e '\nsource ${FSLDIR}/etc/fslconf/fsl.sh\n' >> ${SHELL_PROFILE}
 rm fslinstaller.py
 
 # BIP
-/usr/local/fsl/bin/mamba install -y -n base fsl-bip
+/usr/local/fsl/bin/mamba install -y -n base --override-channels    \
+  -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/development/ \
+  -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/      \
+  -c conda-forge                                                   \
+   fsl-bip
 
 # ROBEX
 ROBEX_URL=https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//\?i_agree\=1\&download_now\=1

.gitlab-ci.yml

@@ -26,8 +26,8 @@ build-dev-docker-image:
     - echo $DOCKER_AUTH_CONFIG > $HOME/.docker/config.json
     - TAG="$(date +%Y%m%d).${CI_COMMIT_SHORT_SHA}"
     - IMAGE="pauldmccarthy/bip-dev"
-    - DOCKERFILE=.docker/Dockerfile
-    - docker build -t "${IMAGE}:${TAG}" -t "${IMAGE}:latest" -f ${DOCKERFILE} ./.docker
+    - DOCKERFILE=.docker/bip-dev/Dockerfile
+    - docker build -t "${IMAGE}:${TAG}" -t "${IMAGE}:latest" -f ${DOCKERFILE} ./.docker/bip-dev
     - docker push "${IMAGE}:${TAG}"
     - docker push "${IMAGE}:latest"