Reduced the numer of dependencies to minimise the installation load

Multiscale-Genomics · Dec 18, 2017 · aa4d936 · aa4d936
1 parent 9a9421a
commit aa4d936
Showing 1 changed file with 40 additions and 40 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -12,12 +12,12 @@ addons:
     packages:
     #system environment
     - make
-    - python-dev
+    # - python-dev
     # - build-essential
     # - libssl-dev
-    - zlib1g-dev
-    - libbz2-dev
-    - libreadline-dev
+    # - zlib1g-dev
+    # - libbz2-dev
+    # - libreadline-dev
     # - libsqlite3-dev
     # - libtiff5-dev
     # - libjpeg8-dev
@@ -39,8 +39,8 @@ addons:
     # - r-base-core
     # - python-rpy2
     # - libcurl4-gnutls-dev
-    - unzip
-    - liblzma-dev
+    # - unzip
+    # - liblzma-dev
     # - libtool
     # - pigz
 
@@ -60,26 +60,26 @@ install:
     - make install
 
     # SAMtools
-    - cd ${HOME}/lib
-    - git clone https://github.com/samtools/samtools.git
-    - cd samtools
-    - autoheader
-    - autoconf -Wno-syntax
-    - ./configure --prefix=${HOME}/lib/samtools
-    - make
-    - make install
+    # - cd ${HOME}/lib
+    # - git clone https://github.com/samtools/samtools.git
+    # - cd samtools
+    # - autoheader
+    # - autoconf -Wno-syntax
+    # - ./configure --prefix=${HOME}/lib/samtools
+    # - make
+    # - make install
 
     # UCSC Tools
     - cd ${HOME}/lib
     - wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed
     - wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig
 
     # bedTools
-    - cd ${HOME}/lib
-    - wget https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz
-    - tar -zxvf bedtools-2.26.0.tar.gz
-    - cd bedtools2
-    - make
+    # - cd ${HOME}/lib
+    # - wget https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz
+    # - tar -zxvf bedtools-2.26.0.tar.gz
+    # - cd bedtools2
+    # - make
 
 before_script :
     - cd ${HOME}/bin
@@ -93,27 +93,27 @@ before_script :
     - ln -s ${HOME}/lib/htslib/bin/htsfile htsfile
     - ln -s ${HOME}/lib/htslib/bin/tabix tabix
 
-    - ln -s ${HOME}/lib/samtools/bin/ace2sam ace2sam
-    - ln -s ${HOME}/lib/samtools/bin/blast2sam.pl blast2sam.pl
-    - ln -s ${HOME}/lib/samtools/bin/bowtie2sam.pl bowtie2sam.pl
-    - ln -s ${HOME}/lib/samtools/bin/export2sam.pl export2sam.pl
-    - ln -s ${HOME}/lib/samtools/bin/interpolate_sam.pl interpolate_sam.pl
-    - ln -s ${HOME}/lib/samtools/bin/maq2sam-long maq2sam-long
-    - ln -s ${HOME}/lib/samtools/bin/maq2sam-short maq2sam-short
-    - ln -s ${HOME}/lib/samtools/bin/md5fa md5fa
-    - ln -s ${HOME}/lib/samtools/bin/md5sum-lite md5sum-lite
-    - ln -s ${HOME}/lib/samtools/bin/novo2sam.pl novo2sam.pl
-    - ln -s ${HOME}/lib/samtools/bin/plot-bamstats plot-bamstats
-    - ln -s ${HOME}/lib/samtools/bin/psl2sam.pl psl2sam.pl
-    - ln -s ${HOME}/lib/samtools/bin/sam2vcf.pl sam2vcf.pl
-    - ln -s ${HOME}/lib/samtools/bin/samtools samtools
-    - ln -s ${HOME}/lib/samtools/bin/samtools.pl samtools.pl
-    - ln -s ${HOME}/lib/samtools/bin/seq_cache_populate.pl seq_cache_populate.pl
-    - ln -s ${HOME}/lib/samtools/bin/soap2sam.pl soap2sam.pl
-    - ln -s ${HOME}/lib/samtools/bin/varfilter.py varfilter.py
-    - ln -s ${HOME}/lib/samtools/bin/wgsim wgsim
-    - ln -s ${HOME}/lib/samtools/bin/wgsim_eval.pl wgsim_eval.pl
-    - ln -s ${HOME}/lib/samtools/bin/zoom2sam.pl zoom2sam.pl
+    # - ln -s ${HOME}/lib/samtools/bin/ace2sam ace2sam
+    # - ln -s ${HOME}/lib/samtools/bin/blast2sam.pl blast2sam.pl
+    # - ln -s ${HOME}/lib/samtools/bin/bowtie2sam.pl bowtie2sam.pl
+    # - ln -s ${HOME}/lib/samtools/bin/export2sam.pl export2sam.pl
+    # - ln -s ${HOME}/lib/samtools/bin/interpolate_sam.pl interpolate_sam.pl
+    # - ln -s ${HOME}/lib/samtools/bin/maq2sam-long maq2sam-long
+    # - ln -s ${HOME}/lib/samtools/bin/maq2sam-short maq2sam-short
+    # - ln -s ${HOME}/lib/samtools/bin/md5fa md5fa
+    # - ln -s ${HOME}/lib/samtools/bin/md5sum-lite md5sum-lite
+    # - ln -s ${HOME}/lib/samtools/bin/novo2sam.pl novo2sam.pl
+    # - ln -s ${HOME}/lib/samtools/bin/plot-bamstats plot-bamstats
+    # - ln -s ${HOME}/lib/samtools/bin/psl2sam.pl psl2sam.pl
+    # - ln -s ${HOME}/lib/samtools/bin/sam2vcf.pl sam2vcf.pl
+    # - ln -s ${HOME}/lib/samtools/bin/samtools samtools
+    # - ln -s ${HOME}/lib/samtools/bin/samtools.pl samtools.pl
+    # - ln -s ${HOME}/lib/samtools/bin/seq_cache_populate.pl seq_cache_populate.pl
+    # - ln -s ${HOME}/lib/samtools/bin/soap2sam.pl soap2sam.pl
+    # - ln -s ${HOME}/lib/samtools/bin/varfilter.py varfilter.py
+    # - ln -s ${HOME}/lib/samtools/bin/wgsim wgsim
+    # - ln -s ${HOME}/lib/samtools/bin/wgsim_eval.pl wgsim_eval.pl
+    # - ln -s ${HOME}/lib/samtools/bin/zoom2sam.pl zoom2sam.pl
 
 # command to run tests
 script: pytest -m "not underdeverlopment"