fix: introduce setup script

PharmGKB · Nov 18, 2024 · 980ffc0 · 980ffc0
1 parent 53cbff9
commit 980ffc0
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diff --git a/bin/setup.sh b/bin/setup.sh
@@ -0,0 +1,220 @@
+#!/usr/bin/env bash
+#
+#  Sets up PharmCAT in the current directory after checking for basic requirements.
+#
+#
+
+set -e
+set -u
+set -o pipefail
+
+PHARMCAT_VERSION="2.15.5"
+# Java 17 = 61 class major version
+MIN_JAVA_VERSION=17
+MIN_JAVA_CLASS_VERSION=61
+MIN_PYTHON_VERSION=3.10
+MIN_BGZIP_VERSION=1.18
+MIN_BCFTOOLS_VERSION=1.18
+
+
+if [[ $TERM && $TERM != 'dumb' ]]; then
+  if command -v tput &>/dev/null; then
+    GREEN=$(tput setaf 2; tput bold)
+    YELLOW=$(tput setaf 3)
+    RED=$(tput setaf 1)
+    NORMAL=$(tput sgr0)
+  fi
+fi
+
+function echo_red() {
+  >&2 echo -e "$RED$*$NORMAL"
+}
+
+function echo_yellow() {
+    >&2 echo -e "$YELLOW$*$NORMAL"
+}
+
+function echo_green() {
+    echo -e "$GREEN$*$NORMAL"
+}
+
+
+# compare function based on https://stackoverflow.com/a/4025065/1063501
+# modified to use echo return values based on https://linuxize.com/post/bash-functions/#return-values
+compare_versions () {
+  if [[ $1 == $2 ]]
+  then
+    echo "="
+    return
+  fi
+  local IFS=.
+  local i ver1=($1) ver2=($2)
+  # fill empty fields in ver1 with zeros
+  for ((i=${#ver1[@]}; i<${#ver2[@]}; i++))
+  do
+    ver1[i]=0
+  done
+  for ((i=0; i<${#ver1[@]}; i++))
+  do
+    if ((10#${ver1[i]:=0} > 10#${ver2[i]:=0}))
+    then
+      echo ">"
+      return
+    fi
+    if ((10#${ver1[i]} < 10#${ver2[i]}))
+    then
+      echo "<"
+      return
+    fi
+  done
+  echo "="
+  return
+}
+
+
+# check for pre-existing preprocessor directory
+if [ -d "preprocessor" ]; then
+    echo_yellow "Found pre-existing preprocessor subdirectory."
+  	echo ""
+    echo_yellow "Please delete this subdirectory and try again."
+    echo ""
+    exit 1
+fi
+
+
+echo "Looking for Java ${MIN_JAVA_VERSION} or greater..."
+# xargs at the end removes newline
+java_version=$(javap -verbose java.lang.String | grep "major version" | cut -d " " -f5 | xargs -d '\r' echo -n)
+if [[ $java_version -lt $MIN_JAVA_CLASS_VERSION ]]; then
+	echo_red "Not found!"
+	echo ""
+	echo_yellow "Please install Java ${MIN_JAVA_VERSION} or greater on your system using your favorite package manager"
+	echo_yellow "and try again."
+	echo ""
+	exit 1
+fi
+
+echo "Looking for Python 3.10 or greater..."
+python_version=$(python3 -c "import platform; print(platform.python_version())")
+op=$(compare_versions $python_version $MIN_PYTHON_VERSION)
+if [[ $op = '<' ]]; then
+	echo_red "Not found!"
+	echo ""
+	echo_yellow "Please install Python ${MIN_PYTHON_VERSION} or greater on your system using your favorite package manager"
+	echo_yellow "and try again."
+	echo ""
+	exit 1
+else
+  echo "  Found Python ${python_version}"
+fi
+
+echo "Looking for bgzip ${MIN_BGZIP_VERSION} or greater..."
+bgzip_version=$(bgzip --version | head -n 1 | awk '{print $3}')
+op=$(compare_versions "${bgzip_version}" $MIN_BGZIP_VERSION)
+if [[ $op = '<' ]]; then
+	echo_red "Not found!"
+	echo ""
+	echo_yellow "Please install bgzip ${MIN_BGZIP_VERSION} or greater on your system and try again."
+	echo ""
+	echo_yellow "bgzip can be found in htslib @ https://www.htslib.org/download/"
+	echo ""
+	exit 1
+else
+  echo "  Found bgzip ${bgzip_version}"
+fi
+
+echo "Looking for bcftools ${MIN_BCFTOOLS_VERSION} or greater..."
+bcftools_version=$(bcftools --version | head -n 1 | awk '{print $2}')
+op=$(compare_versions "${bcftools_version}" $MIN_BCFTOOLS_VERSION)
+if [[ $op = '<' ]]; then
+	echo_red "Not found!"
+	echo ""
+	echo_yellow "Please install bcftools ${MIN_BCFTOOLS_VERSION} or greater on your system and try again."
+	echo ""
+	echo_yellow "bcftools can be found @ https://www.htslib.org/download/"
+	echo ""
+	exit 1
+else
+  echo "  Found bcftools ${bcftools_version}"
+fi
+
+
+RELEASE_URL=https://github.com/PharmGKB/PharmCAT/releases/download/v${PHARMCAT_VERSION}
+JAR_URL=${RELEASE_URL}/pharmcat-${PHARMCAT_VERSION}-all.jar
+SCRIPT_URL=https://raw.githubusercontent.com/PharmGKB/PharmCAT/refs/heads/main/bin/pharmcat
+PREPROCESSOR_URL=${RELEASE_URL}/pharmcat-preprocessor-${PHARMCAT_VERSION}.tar.gz
+
+if command -v curl &>/dev/null; then
+  GET_JAR="curl -fsSL '${JAR_URL}' -o 'pharmcat.jar'"
+  GET_SCRIPT="curl -fsSL '${SCRIPT_URL}' -o 'pharmcat'"
+  GET_PREPROCESSOR="curl -fsSL '${PREPROCESSOR_URL}' -o 'preprocessor.tgz'"
+elif command -v wget &>/dev/null; then
+  GET_JAR="wget '${JAR_URL}' -O 'pharmcat.jar' >/dev/null 2>&1"
+  GET_SCRIPT="wget '${SCRIPT_URL}' -O 'pharmcat' >/dev/null 2>&1"
+  GET_PREPROCESSOR="wget '${PREPROCESSOR_URL}' -O 'preprocessor.tgz' >/dev/null 2>&1"
+else
+  echo_red "ERROR: Cannot find 'curl' nor 'wget' utility --  please install one of them"
+	echo ""
+  exit 1
+fi
+
+
+echo ""
+echo "Downloading PharmCAT jar..."
+set +e
+eval $GET_JAR; status=$?
+set -e
+if [ $status -ne 0 ]; then
+  echo ""
+  echo_red "ERROR: Cannot download PharmCAT jar -- make sure you can connect to the internet"
+  echo ""
+  exit 1
+fi
+
+
+echo ""
+echo "Downloading PharmCAT script..."
+set +e
+eval $GET_SCRIPT; status=$?
+set -e
+if [ $status -ne 0 ]; then
+  echo ""
+  echo_red "ERROR: Cannot download PharmCAT Preprocessor -- make sure you can connect to the internet"
+  echo ""
+  exit 1
+fi
+
+chmod 755 pharmcat
+
+
+echo ""
+echo "Downloading PharmCAT Preprocessor..."
+set +e
+eval $GET_PREPROCESSOR; status=$?
+set -e
+if [ $status -ne 0 ]; then
+  echo ""
+  echo_red "ERROR: Cannot download PharmCAT Preprocessor -- make sure you can connect to the internet"
+  echo ""
+  exit 1
+fi
+
+tar -xzf preprocessor.tgz
+rm preprocessor.tgz
+
+mv preprocessor tmp
+mv -f tmp/* .
+rmdir tmp
+rm -f README.md
+chmod 755 pharmcat_pipeline pharmcat_vcf_preprocessor.py
+
+echo ""
+echo_green "Done!"
+echo ""
+echo "Don't forget to install PharmCAT Preprocessor's Python dependencies."
+echo ""
+echo "You can do so with:"
+echo_yellow "  pip3 install -r requirements.txt"
+echo ""
+echo "Or use your preferred Python virtual environment to do so."
+echo ""
diff --git a/package.json b/package.json
@@ -50,6 +50,29 @@
           ]
         }
       ],
+      [
+        "@google/semantic-release-replace-plugin",
+        {
+          "replacements": [
+            {
+              "files": [
+                "bin/setup.sh"
+              ],
+              "from": "^PHARMCAT_VERSION=.*",
+              "to": "PHARMCAT_VERSION=${nextRelease.version}",
+              "results": [
+                {
+                  "file": "bin/setup.sh",
+                  "hasChanged": true,
+                  "numMatches": 1,
+                  "numReplacements": 1
+                }
+              ],
+              "countMatches": true
+            }
+          ]
+        }
+      ],
       [
         "@google/semantic-release-replace-plugin",
         {
@@ -159,6 +182,7 @@
         {
           "assets": [
             "CHANGELOG.md",
+            "bin/setup.sh",
             "dockstore/pipeline/PharmCAT_Pipeline.wdl",
             "dockstore/pipeline/README.md",
             "docs/index.md",