Compiling and Installing Trinity

Procedure

1. Run the following commands to go to the installation directory and decompress the installation packages:

   cd /path/to/TRINITY
   tar -zxf v2.11.0.tar.gz
   unzip master.zip
   unzip 8ef13ed1fa618186ec3dc04522115c99fdfacda2.zip
   unzip f034f247d5fa1fd9847c390d99bfd918da7d7739.zip
   unzip f5e229dc164823c3ef14e8b8e2ba7d84c8d80e6c.zip
   unzip 1.11.zip

2. Run the following commands to save the source code of Inchworm, Chrysalis, seqtk-trinity, and bamsifter to the corresponding directories in the Tinity source code:

   cp -rf Chrysalis-8ef13ed1fa618186ec3dc04522115c99fdfacda2/* trinityrnaseq-2.11.0/Chrysalis
   cp -rf Inchworm-master/* trinityrnaseq-2.11.0/Inchworm
   cp -rf seqtk-trinity-f5e229dc164823c3ef14e8b8e2ba7d84c8d80e6c/* trinityrnaseq-2.11.0/trinity-plugins/seqtk-trinity
   cp -rf bamsifter-f034f247d5fa1fd9847c390d99bfd918da7d7739/* trinityrnaseq-2.11.0/trinity-plugins/bamsifter
   cp -rf htslib-1.11/* trinityrnaseq-2.11.0/trinity-plugins/bamsifter/htslib

3. Run the following command to decompress ParaFly-0.1.0.tar.gz:

   cd trinityrnaseq-2.11.0/trinity-plugins && tar -zxf ParaFly-0.1.0.tar.gz

4. Run the following commands to replace the parameter -m64 by -mabi=lp64:

   cd /path/to/TRINITY/trinityrnaseq-2.11.0
   sed -i '/tar -zxvf ${PARAFLY_CODE}.tar.gz/d' trinity-plugins/Makefile
   sed -i 's/\-m64/\-mabi=lp64/g' `grep -rl "\-m64" ./`

5. Run the following commands to add the compilation optimization parameters:

   sed -i 's/cmake/cmake -DCMAKE_CXX_FLAGS="-O3 -march=armv8.2-a -mtune=tsv110"/g' ./Chrysalis/Makefile ./Inchworm/Makefile
   sed -i 's/\-fopenmp/-O3 -march=armv8.2-a -mtune=tsv110 -fopenmp/g' ./trinity-plugins/Makefile

6. Run the following command to set the environment variable:

   export PATH=/path/to/CMAKE/bin:$PATH

7. Run the following command to perform the compilation and installation:

   make -j

   If the information shown in the following figure is displayed, the installation is successful: