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Installation from source codes

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make

GNU Make is a program often used for compiling software. It uses a plain text file named makefile or Makefile.

Steps

  1. Unpack the source code archive.

  2. Configure the package. ## Some packages do not have the configure file

  3. Run make to build the programs.

  4. Run make install to install the package. # Optional

❌ Do not run sudo make install

By default, make install will install applications into /usr/local, but regular users do not have permission to write into /usr/lobcal.

The best way is to install applications into your home directory or /depot by passing the option --prefix=TargetDirName to ./configure.

bwa

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

Installation guide from README

git clone https://github.com/lh3/bwa.git
cd bwa; make
./bwa index ref.fa
./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz
./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz

## Load the compiler 
$ module av gcc
$ module load gcc/11.2.0 ## Recommend to load the newest version of gcc
$ cd $HOME
$ mkdir apps 
$ cd apps
$ git clone https://github.com/lh3/bwa.git
$ cd bwa; make

# Add the bwa directory to $PATH
$ export PATH=$PATH:$HOME/apps/bwa
# bwa is ready to use
$ bwa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.18-r1243-dirty
Contact: Heng Li <hli@ds.dfci.harvard.edu>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries (DEPRECATED)

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.

hmmer

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

Installation guide from README

wget http://eddylab.org/software/hmmer/hmmer.tar.gz
tar zxf hmmer.tar.gz
cd hmmer-3.4
./configure --prefix /your/install/path   # replace /your/install/path with what you want, obv 
make
make check                                # optional: run automated tests
make install                              # optional: install HMMER programs, man pages

$ cd $HOME
$ cd apps
# Download source code
$ wget http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz
# Unpack source code archive 
$ tar -xvf hmmer-3.4.tar.gz
$ cd hmmer-3.4
# compile the code
./configure --prefix=$HOME/myapps 
make
make check
make install

# Add the bwa directory to $PATH
$ export PATH=$PATH:$HOME/apps/bin
# hmmer is ready to use
$ hmmsearch -h
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.4 (Aug 2023); http://hmmer.org/
# Copyright (C) 2023 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Usage: hmmsearch [options] <hmmfile> <seqdb>

cmake

CMake is an open-source, cross-platform family of tools designed to build, test, and package software. It controls the software compilation process by generating native build scripts (like Makefiles or project files) for a wide variety of platforms and compilers.

Installation of some bioinformatics applications requires both make and cmake.

RegTools

RegTools integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.

Installation guide from the developer

git clone https://github.com/griffithlab/regtools
cd regtools/
mkdir build
cd build/
cmake ..
make

Installation on HPC

 $ module avail cmake

--------------------- /opt/shared/Modules/modulefiles-rhel6 ------------------------------
   cmake/2.8    cmake/2.8.11.2    cmake/3.2.1    cmake/3.4.3

--------------------- /cluster/tufts/hpc/tools/module ------------------------------------
   cmake/3.18    cmake/3.23_gui (D)

$ module load gcc/11.2.0
$ module load cmake/3.23_gui ## Recommand to use the latest version of cmake
$ cd $HOME/apps
$ git clone https://github.com/griffithlab/regtools
$ cd regtools/
$ mkdir build
$ cd build/
$ cmake ..
$ make

$ export PATH=$PATH:$HOME/apps/regtools/build

DCMAKE_INSTALL_PREFIX

Some applications' installation also has install stage, which will have make intall as the last step. For these installations, we have to include -DCMAKE_INSTALL_PREFIX in the cmake .. step. Below are the common steps for such installations:

module load gcc
module load cmake
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/path/to/install ..
make
make install