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authorBryan Galdrikian <[email protected]>2018-07-30 15:17:29 -0700
committerBryan Galdrikian <[email protected]>2018-07-30 15:17:29 -0700
commita4bb63f12fd702384f9ffcf4ec52003eb5e7bcc9 (patch)
treededa7808bdda29348107df252b2f5b4700b4a27a /buildtools
parentFixing path to BlastTool in README (diff)
downloadblast-a4bb63f12fd702384f9ffcf4ec52003eb5e7bcc9.tar.xz
blast-a4bb63f12fd702384f9ffcf4ec52003eb5e7bcc9.zip
Fixing line endings in buildtools/packman5/packman
Diffstat (limited to 'buildtools')
-rwxr-xr-xbuildtools/packman5/packman198
1 files changed, 99 insertions, 99 deletions
diff --git a/buildtools/packman5/packman b/buildtools/packman5/packman
index 0b10d9e..c16a2a7 100755
--- a/buildtools/packman5/packman
+++ b/buildtools/packman5/packman
@@ -1,99 +1,99 @@
-#!/bin/bash
-
-PM_PACKMAN_VERSION=5.2.1
-
-# Specify where packman command exists
-export PM_INSTALL_PATH=$(dirname ${BASH_SOURCE})
-
-# The packages root may already be configured by the user
-if [ -z "$PM_PACKAGES_ROOT" ]; then
- # Set variable permanently using .profile for this user
- echo "export PM_PACKAGES_ROOT=\$HOME/packman-repo" >> ~/.profile
- # Set variable temporarily in this process so that the following execution will work
- export PM_PACKAGES_ROOT="${HOME}/packman-repo"
-fi
-
-# Ensure the packages root path exists:
-if [ ! -d "$PM_PACKAGES_ROOT" ]; then
- echo "Creating packman packages repository at $PM_PACKAGES_ROOT"
- mkdir -p "$PM_PACKAGES_ROOT"
-fi
-
-# The packman module may be externally configured
-if [ -z "$PM_MODULE_EXT" ]; then
- PM_MODULE_DIR="$PM_PACKAGES_ROOT/packman-common/$PM_PACKMAN_VERSION"
- export PM_MODULE="$PM_MODULE_DIR/packman.py"
-else
- export PM_MODULE="$PM_MODULE_EXT"
-fi
-
-fetch_file_from_s3()
-{
- SOURCE=$1
- SOURCE_URL=http://packman.s3.amazonaws.com/$SOURCE
- TARGET=$2
- echo "Fetching $SOURCE from S3 ..."
- if command -v wget >/dev/null 2>&1; then
- wget --quiet -O$TARGET $SOURCE_URL
- else
- curl -o $TARGET $SOURCE_URL -s -S
- fi
-}
-
-# Ensure the packman package exists:
-if [ ! -f "$PM_MODULE" ]; then
- PM_MODULE_PACKAGE="packman-common@$PM_PACKMAN_VERSION.zip"
- TARGET="/tmp/$PM_MODULE_PACKAGE"
- # We always fetch packman from S3:
- fetch_file_from_s3 $PM_MODULE_PACKAGE $TARGET
- if [ "$?" -eq "0" ]; then
- echo "Unpacking ..."
- mkdir -p "$PM_MODULE_DIR"
- unzip -q $TARGET -d "$PM_MODULE_DIR"
- rm $TARGET
- else
- echo "Failure while fetching packman module from S3!"
- exit 1
- fi
-fi
-
-# For now assume python is installed on the box and we just need to find it
-if command -v python2.7 >/dev/null 2>&1; then
- export PM_PYTHON=python2.7
-elif command -v python2 >/dev/null 2>&1; then
- export PM_PYTHON=python2
-else
- export PM_PYTHON=python
-fi
-
-# Ensure 7za package exists:
-PM_7za_VERSION=16.02.2
-export PM_7za_PATH="$PM_PACKAGES_ROOT/chk/7za/$PM_7za_VERSION"
-if [ ! -f "$PM_7za_PATH" ]; then
- $PM_PYTHON "$PM_MODULE" install 7za $PM_7za_VERSION -r packman:cloudfront
- if [ "$?" -ne 0 ]; then
- echo "Failure while installing required 7za package"
- exit 1
- fi
-fi
-
-# Generate temporary file name for environment variables:
-PM_VAR_PATH=`mktemp -u -t tmp.XXXXX.$$.pmvars`
-
-$PM_PYTHON -u "$PM_MODULE" $* --var-path="$PM_VAR_PATH"
-exit_code=$?
-# Export the variables if the file was used and remove the file:
-if [ -f "$PM_VAR_PATH" ]; then
- while read -r line
- do
- if [ ${#line} -gt 0 ]; then
- export "$line"
- fi
- done < "$PM_VAR_PATH"
- rm -f "$PM_VAR_PATH"
-fi
-
-# Return the exit code from python
-if [ "$exit_code" != 0 ]; then
- exit "$exit_code"
-fi
+#!/bin/bash
+
+PM_PACKMAN_VERSION=5.2.1
+
+# Specify where packman command exists
+export PM_INSTALL_PATH=$(dirname ${BASH_SOURCE})
+
+# The packages root may already be configured by the user
+if [ -z "$PM_PACKAGES_ROOT" ]; then
+ # Set variable permanently using .profile for this user
+ echo "export PM_PACKAGES_ROOT=\$HOME/packman-repo" >> ~/.profile
+ # Set variable temporarily in this process so that the following execution will work
+ export PM_PACKAGES_ROOT="${HOME}/packman-repo"
+fi
+
+# Ensure the packages root path exists:
+if [ ! -d "$PM_PACKAGES_ROOT" ]; then
+ echo "Creating packman packages repository at $PM_PACKAGES_ROOT"
+ mkdir -p "$PM_PACKAGES_ROOT"
+fi
+
+# The packman module may be externally configured
+if [ -z "$PM_MODULE_EXT" ]; then
+ PM_MODULE_DIR="$PM_PACKAGES_ROOT/packman-common/$PM_PACKMAN_VERSION"
+ export PM_MODULE="$PM_MODULE_DIR/packman.py"
+else
+ export PM_MODULE="$PM_MODULE_EXT"
+fi
+
+fetch_file_from_s3()
+{
+ SOURCE=$1
+ SOURCE_URL=http://packman.s3.amazonaws.com/$SOURCE
+ TARGET=$2
+ echo "Fetching $SOURCE from S3 ..."
+ if command -v wget >/dev/null 2>&1; then
+ wget --quiet -O$TARGET $SOURCE_URL
+ else
+ curl -o $TARGET $SOURCE_URL -s -S
+ fi
+}
+
+# Ensure the packman package exists:
+if [ ! -f "$PM_MODULE" ]; then
+ PM_MODULE_PACKAGE="packman-common@$PM_PACKMAN_VERSION.zip"
+ TARGET="/tmp/$PM_MODULE_PACKAGE"
+ # We always fetch packman from S3:
+ fetch_file_from_s3 $PM_MODULE_PACKAGE $TARGET
+ if [ "$?" -eq "0" ]; then
+ echo "Unpacking ..."
+ mkdir -p "$PM_MODULE_DIR"
+ unzip -q $TARGET -d "$PM_MODULE_DIR"
+ rm $TARGET
+ else
+ echo "Failure while fetching packman module from S3!"
+ exit 1
+ fi
+fi
+
+# For now assume python is installed on the box and we just need to find it
+if command -v python2.7 >/dev/null 2>&1; then
+ export PM_PYTHON=python2.7
+elif command -v python2 >/dev/null 2>&1; then
+ export PM_PYTHON=python2
+else
+ export PM_PYTHON=python
+fi
+
+# Ensure 7za package exists:
+PM_7za_VERSION=16.02.2
+export PM_7za_PATH="$PM_PACKAGES_ROOT/chk/7za/$PM_7za_VERSION"
+if [ ! -f "$PM_7za_PATH" ]; then
+ $PM_PYTHON "$PM_MODULE" install 7za $PM_7za_VERSION -r packman:cloudfront
+ if [ "$?" -ne 0 ]; then
+ echo "Failure while installing required 7za package"
+ exit 1
+ fi
+fi
+
+# Generate temporary file name for environment variables:
+PM_VAR_PATH=`mktemp -u -t tmp.XXXXX.$$.pmvars`
+
+$PM_PYTHON -u "$PM_MODULE" $* --var-path="$PM_VAR_PATH"
+exit_code=$?
+# Export the variables if the file was used and remove the file:
+if [ -f "$PM_VAR_PATH" ]; then
+ while read -r line
+ do
+ if [ ${#line} -gt 0 ]; then
+ export "$line"
+ fi
+ done < "$PM_VAR_PATH"
+ rm -f "$PM_VAR_PATH"
+fi
+
+# Return the exit code from python
+if [ "$exit_code" != 0 ]; then
+ exit "$exit_code"
+fi