[release v1.11.4] fix libgff linking

Author: Rob Patro

current_version.txt

@@ -1,3 +1,3 @@
 VERSION_MAJOR 1
 VERSION_MINOR 11
-VERSION_PATCH 0
+VERSION_PATCH 4

doc/source/conf.py

@@ -57,7 +57,7 @@
 # The short X.Y version.
 version = '1.11'
 # The full version, including alpha/beta/rc tags.
-release = '1.11.0'
+release = '1.11.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docker/Dockerfile

@@ -6,7 +6,7 @@ MAINTAINER salmon.maintainer@gmail.com
 
 ENV PACKAGES git gcc make g++ libboost-all-dev liblzma-dev libbz2-dev \
     ca-certificates zlib1g-dev libcurl4-openssl-dev curl unzip autoconf apt-transport-https ca-certificates gnupg software-properties-common wget
-ENV SALMON_VERSION 1.11.0
+ENV SALMON_VERSION 1.11.4
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

docker/build_test.sh

@@ -1,3 +1,3 @@
 #! /bin/bash
-SALMON_VERSION=1.11.0
+SALMON_VERSION=1.11.4
 TMPDIR=/mnt/scratch7/DELETE_ME_TEMP docker build --no-cache -t combinelab/salmon:${SALMON_VERSION} -t combinelab/salmon:latest .

scripts/bump_version.sh

@@ -2,9 +2,9 @@
 
 HERE="$( cd "$(dirname "$0")" ; pwd -P )"
 
-major_v=`${HERE}/../build/using-sshash/src/salmon -v | cut -d ' ' -f 2 | cut -d '.' -f 1`
-minor_v=`${HERE}/../build/using-sshash/src/salmon -v | cut -d ' ' -f 2 | cut -d '.' -f 2`
-patch_v=`${HERE}/../build/using-sshash/src/salmon -v | cut -d ' ' -f 2 | cut -d '.' -f 3`
+major_v=`${HERE}/../build/src/salmon -v | cut -d ' ' -f 2 | cut -d '.' -f 1`
+minor_v=`${HERE}/../build/src/salmon -v | cut -d ' ' -f 2 | cut -d '.' -f 2`
+patch_v=`${HERE}/../build/src/salmon -v | cut -d ' ' -f 2 | cut -d '.' -f 3`
 
 echo "VERSION : ${major_v}.${minor_v}.${patch_v}"