add qsv to docker image (#26)

* update miniconda version

* add script to install qsv from tagged release; call in Dockerfile

add script to install qsv within docker image from tagged release (not yet available via apt repo)

* bump actions/checkout v3 -> v4

* bump Ubuntu baseimage for this (base)image: jammy-20230126 -> jammy-20240227

.github/workflows/docker-image.yml

@@ -13,6 +13,6 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Build the Docker image
       run: docker build . --file Dockerfile --tag my-image-name:$(date +%s)

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:jammy-20230126
+FROM ubuntu:jammy-20240227
 
 LABEL maintainer "viral-ngs team <viral-ngs@broadinstitute.org>"
 
@@ -23,6 +23,9 @@ RUN /opt/docker/install-udocker.sh
 # install DNAnexus SDK and UA
 RUN /opt/docker/install-dnanexus-cli.sh
 
+# install qsv (binary for manipulation and query of tabular data files like tsv)
+RUN /opt/docker/install-qsv.sh
+
 # install miniconda3 with our default channels and no other packages
 ENV MINICONDA_PATH="/opt/miniconda"
 RUN /opt/docker/install-miniconda.sh

install-miniconda.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 set -e -o pipefail
 
-MINICONDA_VERSION="py310_23.1.0-1"
+MINICONDA_VERSION="py310_24.1.2-0"
 MINICONDA_URL="https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh"
 
 # download and run miniconda installer script

install-qsv.sh

@@ -0,0 +1,75 @@
+#!/bin/bash
+
+# This installs qsv:
+#   "a command line program for querying, indexing, slicing, analyzing, filtering, enriching,
+#    transforming, sorting, validating & joining CSV files"
+#
+# Additional information available here:
+#   https://github.com/jqnatividad/qsv
+#
+# Additional information on available releases (including the latest versions) available here:
+#   https://github.com/jqnatividad/qsv/releases
+
+QSV_BINARY=qsvlite # "qsv" is the binary with all features enabled; "qsvlite" has extra features disabled and is much smaller in size
+QSV_VERSION=0.123.0
+
+case "$(uname -m)" in
+  x86_64)
+    CPU_ARCH="x86_64"
+    ;;
+  arm64 | aarch64)
+    CPU_ARCH="aarch64" #"aarch64" for Apple Silicon and other ARM-based CPUs
+    ;;
+  *)
+    CPU_ARCH="unknown"
+    echo "Unknown CPU architecture returned by uname -m: '${CPU_ARCH}'" >&2
+    exit 1
+    ;;
+esac
+
+case "$(uname -s)" in
+  Linux)
+    OS_BUILD_TYPE="unknown-linux-gnu" # "unknown-linux-musl" for Linux platforms where libc compatability is an issue, otherwise "unknown-linux-gnu"
+    ;;
+  Darwin)
+    OS_BUILD_TYPE="apple-darwin"
+    ;;
+  *)
+    OS_BUILD_TYPE="unknown"
+    echo "Unknown OS type returned by uname -s: '${OS_BUILD_TYPE}'" >&2
+    exit 1
+    ;;
+esac
+
+if ! command -v curl &> /dev/null; then
+    echo "curl is required but it does not appear to be installed" >&2
+    exit 1
+fi
+
+PACKAGE_ZIP=qsv-${QSV_VERSION}-${CPU_ARCH}-${OS_BUILD_TYPE}.zip
+
+echo "Downloading binary for ${OS_BUILD_TYPE} built for ${CPU_ARCH}: ${PACKAGE_ZIP}"
+curl --silent --location --output $PACKAGE_ZIP https://github.com/jqnatividad/qsv/releases/download/${QSV_VERSION}/${PACKAGE_ZIP}
+
+# unzip only the qsv binary to its final location (the zip archive also contains alternate builds)
+unzip -o -d /usr/local/bin $PACKAGE_ZIP ${QSV_BINARY}
+rm $PACKAGE_ZIP
+
+chmod 755 /usr/local/bin/${QSV_BINARY}
+
+# if copying in an alternate build of qsv, symlink it to "qsv"
+if [[ "$QSV_BINARY" != "qsv" ]]; then
+    if [ ! -f /usr/local/bin/qsv ]; then
+        ln -s /usr/local/bin/${QSV_BINARY} /usr/local/bin/qsv
+    fi
+fi
+
+hash -r
+
+if ! command -v qsv &> /dev/null; then
+    echo "The qsv installation seems to have failed" >&2
+    exit 1
+else
+    echo "qsv installation successful."
+fi
+