Installing and compiling examples
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Go back to parent page Introduction to Linux for bioinformatics
Contents
tsne, a dimensionality reduction tool
The home page of tsne provides a binary to be downloaded to run the program.
| Download the binary file from their website, unpack it and run it. |
|---|
| Looking for the downloads on the page, you can find the compressed tarball download link |
| Download and uncompress. The archive contains one file only. |
Check the execute permissions and test whether you can execute tSNE properly.
$ ls -l tSNE_linux -rwxr-xr-x 1 joachim joachim 526367 Jun 2 2008 tSNE_linux $ ./tSNE_linux Detected unknown processor (with SSSE3) on 2372 MHz. Please note that this software runs faster on Intel processors! Error: could not open data file. |
| It runs fine! |
mcl, simple compiling of a clustering tool
MCL is a command line tool for clustering data. Download it from http://micans.org/mcl/ and try to install it.
Quip, a tool to compress fastq files
Download the compressed tar ball at this link. Copy to /opt and extract the tar ball.
$ pwd /home/joachim/Downloads $ wget http://homes.cs.washington.edu/~dcjones/quip/quip-1.1.8.tar.gz --2013-10-28 11:22:40-- http://homes.cs.washington.edu/~dcjones/quip/quip-1.1.8.tar.gz Resolving homes.cs.washington.edu (homes.cs.washington.edu)... 128.208.3.226 Connecting to homes.cs.washington.edu (homes.cs.washington.edu)|128.208.3.226|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 271626 (265K) [application/x-gzip] Saving to: `quip-1.1.8.tar.gz' 100%[======================================>] 271,626 290K/s in 0.9s 2013-10-28 11:22:42 (290 KB/s) - `quip-1.1.8.tar.gz' saved [271626/271626] $ sudo cp quip-1.1.8.tar.gz /opt [sudo] password for joachim: $ cd /opt $ ls fastQValidator_0.1.1a firefox quip-1.1.8.tar.gz FastQValidatorLibStatGen.0.1.1a.tgz mint-flashplugin-11 $ sudo tar xvfz quip-1.1.8.tar.gz quip-1.1.8/ quip-1.1.8/aclocal.m4 quip-1.1.8/._ar-lib quip-1.1.8/ar-lib quip-1.1.8/._compile quip-1.1.8/compile quip-1.1.8/config.guess quip-1.1.8/config.sub quip-1.1.8/configure quip-1.1.8/configure.ac quip-1.1.8/COPYING quip-1.1.8/._depcomp quip-1.1.8/depcomp quip-1.1.8/._install-sh quip-1.1.8/install-sh quip-1.1.8/m4/ quip-1.1.8/Makefile.am quip-1.1.8/Makefile.in quip-1.1.8/._missing quip-1.1.8/missing quip-1.1.8/quip-format.md quip-1.1.8/quip.1 quip-1.1.8/README.md quip-1.1.8/src/ quip-1.1.8/test-driver quip-1.1.8/tests/ quip-1.1.8/tests/bammd5.c quip-1.1.8/tests/fastqmd5.c quip-1.1.8/tests/Makefile.am quip-1.1.8/tests/Makefile.in quip-1.1.8/tests/md5.c quip-1.1.8/tests/md5.h quip-1.1.8/tests/random_fastq.c quip-1.1.8/src/ac.c quip-1.1.8/src/ac.h quip-1.1.8/src/assembler.c quip-1.1.8/src/assembler.h quip-1.1.8/src/bloom.c quip-1.1.8/src/bloom.h quip-1.1.8/src/config.h.in quip-1.1.8/src/crc64.c quip-1.1.8/src/crc64.h quip-1.1.8/src/crc64_table_be.h quip-1.1.8/src/crc64_table_le.h quip-1.1.8/src/dist.c quip-1.1.8/src/dist.h quip-1.1.8/src/dist_impl.c quip-1.1.8/src/dist_impl.h quip-1.1.8/src/dist_template_off.h quip-1.1.8/src/dist_template_on.h quip-1.1.8/src/fastqfmt.c quip-1.1.8/src/fastqfmt.h quip-1.1.8/src/idenc.c quip-1.1.8/src/idenc.h quip-1.1.8/src/kmer.c quip-1.1.8/src/kmer.h quip-1.1.8/src/kmerhash.c quip-1.1.8/src/kmerhash.h quip-1.1.8/src/Makefile.am quip-1.1.8/src/Makefile.in quip-1.1.8/src/misc.c quip-1.1.8/src/misc.h quip-1.1.8/src/qualenc.c quip-1.1.8/src/qualenc.h quip-1.1.8/src/quip.c quip-1.1.8/src/quip.h quip-1.1.8/src/quipfmt.c quip-1.1.8/src/quipfmt.h quip-1.1.8/src/quiplib.c quip-1.1.8/src/sam/ quip-1.1.8/src/samfmt.c quip-1.1.8/src/samfmt.h quip-1.1.8/src/samopt.c quip-1.1.8/src/samopt.h quip-1.1.8/src/samoptenc.h quip-1.1.8/src/seqenc.c quip-1.1.8/src/seqenc.h quip-1.1.8/src/seqmap.c quip-1.1.8/src/seqmap.h quip-1.1.8/src/strmap.c quip-1.1.8/src/strmap.h quip-1.1.8/src/twobit.c quip-1.1.8/src/twobit.h quip-1.1.8/src/version.h quip-1.1.8/src/version.h.in quip-1.1.8/src/sam/bam.c quip-1.1.8/src/sam/bam.h quip-1.1.8/src/sam/bam_aux.c quip-1.1.8/src/sam/bam_endian.h quip-1.1.8/src/sam/bam_import.c quip-1.1.8/src/sam/bgzf.c quip-1.1.8/src/sam/bgzf.h quip-1.1.8/src/sam/khash.h quip-1.1.8/src/sam/kseq.h quip-1.1.8/src/sam/kstring.c quip-1.1.8/src/sam/kstring.h quip-1.1.8/src/sam/sam.c quip-1.1.8/src/sam/sam.h quip-1.1.8/src/sam/sam_header.c quip-1.1.8/src/sam/sam_header.h quip-1.1.8/m4/acx_pthread.m4 $ ls fastQValidator_0.1.1a firefox quip-1.1.8 FastQValidatorLibStatGen.0.1.1a.tgz mint-flashplugin-11 quip-1.1.8.tar.gz
Compile the program by following the instructions on their website.
$ cd /opt/quip-1.1.8 $ ./configure ... $ sudo make ... $ cd src $ ./quip $ ./quip quip: stdin: assuming input in FASTQ. quip: stdin: refusing to write compressed data to your terminal screen. Use -f is you really want to do this. (Hint: you don't.) $ quip No command 'quip' found, did you mean: Command 'quiz' from package 'bsdgames' (universe) quip: command not found $ sudo ln -s /opt/quip-1.1.8/src/quip /usr/local/bin $ quip quip: stdin: assuming input in FASTQ. quip: stdin: refusing to write compressed data to your terminal screen. Use -f is you really want to do this. (Hint: you don't.) $ ls -l /usr/local/bin/quip lrwxrwxrwx 1 root root 24 Oct 28 11:57 /usr/local/bin/quip -> /opt/quip-1.1.8/src/quip
If you get errors, read them: the important line here is zlib.h: No such file or directory. This usually means some software package on which the tool is dependent is not installed. Some searching on the internet (include your distro name, and the error message) reveals:
sudo apt-get install libssl-dev cmake g++
fastQValidator
A useful package is fastQValidator, a small tool to validate your fastq sequences. [You can't believe how many mistakes can be made in the .fastq format]. Install this similarly as Quip above.
Download the compressed tar ball at this link. Extract the tar ball to /opt.
$ pwd /home/joachim/Downloads $ wget http://genome.sph.umich.edu/w/images/2/20/FastQValidatorLibStatGen.0.1.1a.tgz --2013-10-28 10:51:28-- http://genome.sph.umich.edu/w/images/2/20/FastQValidatorLibStatGen.0.1.1a.tgz Resolving genome.sph.umich.edu (genome.sph.umich.edu)... 141.211.8.98 Connecting to genome.sph.umich.edu (genome.sph.umich.edu)|141.211.8.98|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 548190 (535K) [application/x-gzip] Saving to: `FastQValidatorLibStatGen.0.1.1a.tgz' 100%[=========================================================>] 548,190 129K/s in 4.3s 2013-10-28 10:51:32 (124 KB/s) - `FastQValidatorLibStatGen.0.1.1a.tgz' saved [548190/548190] $ sudo cp FastQValidatorLibStatGen.0.1.1a.tgz /opt $ cd /opt $ ls FastQValidatorLibStatGen.0.1.1a.tgz firefox mint-flashplugin-11 $ sudo tar xvfz FastQValidatorLibStatGen.0.1.1a.tgz fastQValidator_0.1.1a/fastQValidator/ fastQValidator_0.1.1a/fastQValidator/Makefile.inc fastQValidator_0.1.1a/fastQValidator/Makefile ... fastQValidator_0.1.1a/libStatGen/general/MathMatrix.cpp fastQValidator_0.1.1a/libStatGen/general/MemoryMap.cpp fastQValidator_0.1.1a/libStatGen/general/FortranFormat.h fastQValidator_0.1.1a/libStatGen/general/Sort.h $ ls -lh total 548K drwxr-xr-x 4 root root 4.0K Oct 28 10:53 fastQValidator_0.1.1a -rw-r--r-- 1 root root 536K Oct 28 10:52 FastQValidatorLibStatGen.0.1.1a.tgz drwxr-xr-x 4 root root 4.0K May 3 2012 firefox drwxr-xr-x 2 root root 4.0K Oct 8 10:25 mint-flashplugin-11
Compile the program by following the instructions on their website.
$ cd fastQValidator_0.1.1a/ $ sudo make all make[1]: Entering directory `/opt/fastQValidator_0.1.1a/libStatGen' make[2]: Entering directory `/opt/fastQValidator_0.1.1a/libStatGen/samtools' ln -s ../samtools/bgzf.h ../include/bgzf.h ln -s ../samtools/knetfile.h ../include/knetfile.h ln -s ../samtools/khash.h ../include/khash.h ln -s ../samtools/bam.h ../include/bam.h mkdir -p obj gcc -O4 -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o -c bgzf.c In file included from bgzf.c:37:0: bgzf.h:30:18: fatal error: zlib.h: No such file or directory compilation terminated. make[2]: *** [obj/bgzf.o] Error 1 make[2]: Leaving directory `/opt/fastQValidator_0.1.1a/libStatGen/samtools' make[1]: *** [samtools] Error 2 make[1]: Leaving directory `/opt/fastQValidator_0.1.1a/libStatGen' make: *** [libStatGen/] Error 2
If you get errors, read them: the important line here is zlib.h: No such file or directory. This usually means some software package on which the tool is dependent is not installed. Some searching on the internet (include your distro name, and the error message) reveals: [ this link
sudo apt-get install libssl-dev cmake g++
Go back to parent page Introduction to Linux for bioinformatics
