chkuo@koa[~]$ sudo apt install gcc chkuo@koa[~]$ sudo apt install g++ chkuo@koa[~]$ sudo apt install build-essential
# installation chkuo@koa[~]$ sudo apt install openmpi-bin openmpi-doc libopenmpi-dev # to use mpi # 1. prepare '~/.mpd.conf' in the home directory # This file must has the permission set to 600 # and contains one line: MPD_SECRETWORD=<secret> # <secret> is a string (for example, your username) # 2. prepare a command script that contains the instruction to run the program # 3. use 'mpirun' to execute the .sh file # the '-np' option specifies the number of processors to use mpirun -np 8 PROGRAM < COMMAND > LOG &
# perl-doc chkuo@koa[~]$ sudo apt-get install perl-doc # bioperl chkuo@koa[~]$ sudo apt install bioperl # 2018/12/19; ubuntu 18.04.1 # install missing module chkuo@koa[~]$ sudo perl -e shell -MCPAN cpan[1]> install Bio::SearchIO::blastxml chkuo@koa[~]$ perldoc -l Bio::SearchIO::blastxml /usr/local/share/perl/5.26.1/Bio/SearchIO/blastxml.pm
# 2018/12/18; Ubuntu 18.04.1 # python2 chkuo@koa[~]$ python --version Python 2.7.15rc1 # install pip for python package management chkuo@koa[~]$ sudo apt install python-pip chkuo@koa[~]$ pip -V pip 9.0.1 from /usr/lib/python2.7/dist-packages (python 2.7) # install NumPy; required for biopython chkuo@koa[~]$ sudo pip install numpy chkuo@koa[~]$ sudo pip show numpy Name: numpy Version: 1.15.4 Summary: NumPy: array processing for numbers, strings, records, and objects. Home-page: http://www.numpy.org Author: Travis E. Oliphant et al. Author-email: None License: BSD Location: /usr/local/lib/python2.7/dist-packages Requires: # install biopython chkuo@koa[~]$ sudo pip install biopython chkuo@koa[~]$ sudo pip show biopython Name: biopython Version: 1.72 Summary: Freely available tools for computational molecular biology. Home-page: https://biopython.org/ Author: The Biopython Contributors Author-email: biopython@biopython.org License: UNKNOWN Location: /usr/local/lib/python2.7/dist-packages Requires: numpy # PyVCF # https://pyvcf.readthedocs.io/en/latest/index.html chkuo@koa[~]$ sudo pip install pyvcf chkuo@koa[~]$ sudo pip show pyvcf Name: PyVCF Version: 0.6.8 Summary: Variant Call Format (VCF) parser for Python Home-page: https://github.com/jamescasbon/PyVCF Author: James Casbon and @jdoughertyii Author-email: casbon@gmail.com License: UNKNOWN Location: /usr/local/lib/python2.7/dist-packages Requires: setuptools # python3 chkuo@koa[~]$ python3 --version Python 3.6.7 chkuo@koa[~]$ sudo apt install python3-pip chkuo@koa[~]$ pip3 -V pip 9.0.1 from /usr/lib/python3/dist-packages (python 3.6) chkuo@koa[~]$ sudo pip3 install numpy Successfully installed numpy-1.15.4 chkuo@koa[~]$ sudo pip3 install biopython Successfully installed biopython-1.72 chkuo@koa[~]$ sudo pip3 install pyvcf Successfully installed pyvcf-0.6.8 # seqmagick # https://github.com/fhcrc/seqmagick chkuo@koa[~]$ sudo pip3 install seqmagick Successfully installed seqmagick-0.7.0 # install panda package on 2024/07/29 hychang@koa[~]$ sudo pip3 install pandas Successfully installed pandas-1.3.5 pytz-2024.1 hychang@koa[~]$ sudo pip3 -V pip 22.2.2 from /usr/local/lib/python3.7/dist-packages/pip (python 3.7)
# installation on koa, 2018/12/14, Ubuntu 18.04 # install r-base chkuo@koa[~]$ sudo apt install r-base # check version chkuo@koa[~]$ R --version R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
chuan@koa[/usr/local]$ sudo wget https://cran.r-project.org/src/base/R-3/R-3.6.3.tar.gz chuan@koa[/usr/local]$ sudo tar -zxf R-3.6.3.tar.gz chuan@koa[/usr/local]$ cd R-3.6.3 chuan@koa[/usr/local/R-3.6.3]$ sudo ./configure chuan@koa[/usr/local/R-3.6.3]$ sudo make chuan@koa[/usr/local/R-3.6.3]$ bin/R --version R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
chkuo@koa[~]$ sudo R > source("http://bioconductor.org/biocLite.R") > biocLite() > biocLite("NOISeq") > biocLite("ShortRead")
#!/bin/bash # # ncbi_tax.3.sh; 2021/06/25; chkuo # # download NCBI taxonomy db # # prefix: data dir prefix='/data/ncbi' # suffix: date (YYYYMMDD) suffix="$(date +%Y%m%d)" taxonomy_dir="${prefix}/taxonomy_${suffix}" taxonomy_log="${prefix}/taxonomy_${suffix}.log" taxonomy_err="${prefix}/taxonomy_${suffix}.err" date > $taxonomy_log mkdir -p $taxonomy_dir cd $taxonomy_dir rsync --copy-links --times --verbose rsync://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz.md5 $taxonomy_dir 1>> $taxonomy_log 2>> $taxonomy_err rsync --copy-links --times --verbose rsync://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz $taxonomy_dir 1>> $taxonomy_log 2>> $taxonomy_err md5sum -c taxdump.tar.gz.md5 1>> $taxonomy_log 2>> $taxonomy_err tar -xzvf taxdump.tar.gz 1>> $taxonomy_log 2>> $taxonomy_err rm taxdump.tar.gz.md5 rm taxdump.tar.gz date >> $taxonomy_log exit
#!/bin/bash # # ncbi_nt.3.sh; 2021/06/25; chkuo # # download NCBI nt db # # prefix: data dir prefix='/data/ncbi' # suffix: date (YYYYMMDD) suffix="$(date +%Y%m%d)" nt_dir="${prefix}/nt_${suffix}" nt_log="${prefix}/nt_${suffix}.log" nt_err="${prefix}/nt_${suffix}.err" date > $nt_log mkdir -p $nt_dir cd $nt_dir rsync --copy-links --times --verbose rsync://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz.md5 $nt_dir 1>> $nt_log 2>> $nt_err rsync --copy-links --times --verbose rsync://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz $nt_dir 1>> $nt_log 2>> $nt_err md5sum -c *.md5 1>> $nt_log 2>> $nt_err for i in *.tar.gz; do tar -xzvf $i 1>> $nt_log 2>> $nt_err; done rm *.tar.gz.md5 rm *.tar.gz date >> $nt_log exit
#!/bin/bash # # ncbi_nr.3.sh; 2021/06/25; chkuo # # download NCBI nr db # # prefix: data dir prefix='/data/ncbi' # suffix: date (YYYYMMDD) suffix="$(date +%Y%m%d)" nr_dir="${prefix}/nr_${suffix}" nr_log="${prefix}/nr_${suffix}.log" nr_err="${prefix}/nr_${suffix}.err" date > $nr_log mkdir -p $nr_dir cd $nr_dir rsync --copy-links --times --verbose rsync://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz.md5 $nr_dir 1>> $nr_log 2>> $nr_err rsync --copy-links --times --verbose rsync://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz $nr_dir 1>> $nr_log 2>> $nr_err md5sum -c *.md5 1>> $nr_log 2>> $nr_err for i in *.tar.gz; do tar -xzvf $i 1>> $nr_log 2>> $nr_err; done rm *.tar.gz.md5 rm *.tar.gz date >> $nr_log exit
# 2022/09/19; chkuo chkuo@koa[/usr/local]$ sudo pip install ffq
# 2022/09/19; chkuo chkuo@koa[/usr/local]$ sudo wget --output-document sratoolkit.tar.gz https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz chkuo@koa[/usr/local]$ sudo tar -vxzf sratoolkit.tar.gz # set "/data/tmp" as the repository directory
# 2021/06/22; chkuo chkuo@koa[/usr/local]$ sudo wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.11.0/ncbi-blast-2.11.0+-x64-linux.tar.gz chkuo@koa[/usr/local]$ sudo wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.11.0/ncbi-blast-2.11.0+-x64-linux.tar.gz.md5 chkuo@koa[/usr/local]$ md5sum -c ncbi-blast-2.11.0+-x64-linux.tar.gz.md5 chkuo@koa[/usr/local]$ sudo tar -xzf ncbi-blast-2.11.0+-x64-linux.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root ncbi-blast-2.11.0+/
chkuo@koa[/usr/local/bin]$ sudo wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat chkuo@koa[/usr/local/bin]$ sudo chmod 755 blat
Markov cluster algorithm, or MCL, is a clustering algorithm designed by Stijn van Dongen (see the official website here: http://www.micans.org/mcl/).
In bioinformatics, it is useful for defining orthologs based on a similarity graph generated by all-against-all BLAST search.
The installation is quite straightforward:
chkuo@koa[/usr/local]$ sudo wget http://www.micans.org/mcl/src/mcl-latest.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf mcl-latest.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root mcl-14-137 chkuo@koa[/usr/local]$ sudo chmod 755 mcl-14-137 chkuo@koa[/usr/local]$ cd mcl-14-137/ chkuo@koa[/usr/local/mcl-14-137]$ sudo ./configure chkuo@koa[/usr/local/mcl-14-137]$ sudo make chkuo@koa[/usr/local/mcl-14-137]$ sudo make check chkuo@koa[/usr/local/mcl-14-137]$ sudo make install chkuo@koa[/usr/local/mcl-14-137]$ which mcl /usr/local/bin/mcl
chuan@koa[/usr/local]$ sudo git clone https://github.com/JLSteenwyk/orthofisher.git chuan@koa[/usr/local]$ cd orthofisher chuan@koa[/usr/local]$ sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 1 # change python2 to python3 as default chuan@koa[/usr/local]$ sudo make install
chkuo@koa[/usr/local]$ sudo wget http://downloads.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz chkuo@koa[/usr/local]$ sudo tar -xzvf MUMmer3.23.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root MUMmer3.23 chkuo@koa[/usr/local]$ cd MUMmer3.23/ chkuo@koa[/usr/local/MUMmer3.23]$ sudo make chkuo@koa[/usr/local/MUMmer3.23]$ sudo make check chkuo@koa[/usr/local/MUMmer3.23]$ sudo make install chkuo@koa[/usr/local/MUMmer3.23]$ sudo ln -s /usr/local/MUMmer3.23/delta-filter /usr/local/bin/delta-filter chkuo@koa[/usr/local/MUMmer3.23]$ sudo ln -s /usr/local/MUMmer3.23/mummer /usr/local/bin/mummer chkuo@koa[/usr/local/MUMmer3.23]$ sudo ln -s /usr/local/MUMmer3.23/nucmer /usr/local/bin/nucmer chkuo@koa[/usr/local/MUMmer3.23]$ sudo ln -s /usr/local/MUMmer3.23/show-coords /usr/local/bin/show-coords chkuo@koa[/usr/local/MUMmer3.23]$ sudo ln -s /usr/local/MUMmer3.23/mummerplot /usr/local/bin/mummerplot
chkuo@koa[/usr/local]$ sudo wget http://downloads.sourceforge.net/project/gnuplot/gnuplot/5.2.5/gnuplot-5.2.5.tar.gz chkuo@koa[/usr/local]$ sudo tar -xzvf gnuplot-5.2.5.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root gnuplot-5.2.5 chkuo@koa[/usr/local]$ cd gnuplot-5.2.5/ chkuo@koa[/usr/local/gnuplot-5.2.5]$ sudo ./configure chkuo@koa[/usr/local/gnuplot-5.2.5]$ sudo make chkuo@koa[/usr/local/gnuplot-5.2.5]$ sudo make install
chkuo@koa[/usr/local/bin]$ sudo wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64 chkuo@koa[/usr/local/bin]$ sudo chmod 755 muscle3.8.31_i86linux64 chkuo@koa[/usr/local/bin]$ sudo ln -s muscle3.8.31_i86linux64 muscle
chkuo@koa[/usr/local]$ sudo wget http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z chkuo@koa[/usr/local]$ sudo gunzip Gblocks_Linux64_0.91b.tar.Z chkuo@koa[/usr/local]$ sudo tar -xvf Gblocks_Linux64_0.91b.tar chkuo@koa[/usr/local]$ sudo chown -R root:root Gblocks_0.91b/ chkuo@koa[/usr/local]$ sudo chmod -R a+rx Gblocks_0.91b/ chkuo@koa[/usr/local]$ sudo ln -s /usr/local/Gblocks_0.91b/Gblocks /usr/local/bin/Gblocks
chkuo@koa[/usr/local]$ sudo wget http://www.bork.embl.de/pal2nal/distribution/pal2nal.v14.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf pal2nal.v14.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root pal2nal.v14 chkuo@koa[/usr/local]$ sudo ln -s /usr/local/pal2nal.v14 /usr/local/pal2nal
# 2023/05/19 chkuo@koa[/usr/local]$ sudo wget https://github.com/abacus-gene/paml/releases/download/v4.10.6/paml-4.10.6-linux-X86_64.tgz chkuo@koa[/usr/local]$ sudo tar xzf paml-4.10.6-linux-X86_64.tgz chkuo@koa[/usr/local]$ sudo chown -R root:root paml-4.10.6 chkuo@koa[/usr/local]$ sudo chmod -R 755 paml-4.10.6 chkuo@koa[/usr/local]$ cd paml-4.10.6/src chkuo@koa[/usr/local/paml-4.10.6/src]$ sudo make -f Makefile chkuo@koa[/usr/local/paml-4.10.6/src]$ sudo rm *.o chkuo@koa[/usr/local/paml-4.10.6/src]$ sudo mv baseml basemlg chi2 codeml evolver infinitesites mcmctree pamp yn00 ../bin
# required packages chkuo@koa[~]$ sudo apt install default-jdk chkuo@koa[~]$ sudo apt install ant # installation chkuo@koa[/usr/local]$ sudo wget https://github.com/ddarriba/jmodeltest2/files/157117/jmodeltest-2.1.10.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf jmodeltest-2.1.10.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root jmodeltest-2.1.10
sudo apt install libx11-dev sudo apt install libxaw7-dev
Phylip installation:
chkuo@koa[/usr/local]$ sudo wget http://evolution.gs.washington.edu/phylip/download/phylip-3.697.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf phylip-3.697.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root phylip-3.697 chkuo@koa[/usr/local]$ sudo ln -s /usr/local/phylip-3.697 /usr/local/phylip chkuo@koa[/usr/local]$ cd /usr/local/phylip/src chkuo@koa[/usr/local/phylip/src]$ sudo make -f Makefile.unx install
After installation, prepare 3 empty files (outdist, outfile, and outtree) in the home directory (~/). These are the default output files used by PHYLIP. By having these files in the home directory, PHYLIP will ask for custom output filenames, which will be answered by our command scripts.
chkuo@koa[/usr/local]$ sudo wget https://github.com/stephaneguindon/phyml/archive/v3.3.20180621.tar.gz chkuo@koa[/usr/local]$ sudo tar -xzvf v3.3.20180621.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root phyml-3.3.20180621 chkuo@koa[/usr/local]$ cd phyml-3.3.20180621 chkuo@koa[/usr/local/phyml-3.3.20180621]$ sudo ./configure --enable-phyml chkuo@koa[/usr/local/phyml-3.3.20180621]$ sudo make chkuo@koa[/usr/local/phyml-3.3.20180621]$ sudo make install
chkuo@koa[/usr/local]$ sudo wget https://github.com/stamatak/standard-RAxML/archive/v8.2.12.tar.gz chkuo@koa[/usr/local]$ sudo tar -xzvf v8.2.12.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root standard-RAxML-8.2.12 chkuo@koa[/usr/local]$ cd standard-RAxML-8.2.12/ chkuo@koa[/usr/local/standard-RAxML-8.2.12]$ sudo make -f Makefile.AVX.gcc chkuo@koa[/usr/local/standard-RAxML-8.2.12]$ sudo rm *.o
chkuo@koa[/usr/local/bin]$ sudo wget http://www.microbesonline.org/fasttree/FastTree chkuo@koa[/usr/local/bin]$ sudo chmod 755 FastTree
chkuo@koa[/usr/local]$ sudo wget http://www.tree-puzzle.de/tree-puzzle-5.2.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf tree-puzzle-5.2.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root tree-puzzle-5.2 chkuo@koa[/usr/local]$ sudo chmod -R go-w tree-puzzle-5.2 chkuo@koa[/usr/local/tree-puzzle-5.2]$ sudo ./configure chkuo@koa[/usr/local/tree-puzzle-5.2]$ sudo make chkuo@koa[/usr/local/tree-puzzle-5.2]$ sudo make check chkuo@koa[/usr/local/tree-puzzle-5.2]$ sudo make install chkuo@koa[/usr/local/tree-puzzle-5.2]$ sudo make clean chkuo@koa[/usr/local/tree-puzzle-5.2]$ which puzzle /usr/local/bin/puzzle
# prerequisite chkuo@koa[/usr/local]$ sudo apt install build-essential autoconf automake libtool git pkg-config # require BEAGLE # https://code.google.com/p/beagle-lib chkuo@koa[/usr/local]$ sudo wget https://github.com/beagle-dev/beagle-lib/archive/v3.1.2.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf beagle-lib-3.1.2 chkuo@koa[/usr/local]$ sudo chown -R root:root beagle-lib-3.1.2 chkuo@koa[/usr/local]$ cd beagle-lib-3.1.2 chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo ./autogen.sh chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo ./configure --prefix=/usr/local chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo make chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo make check chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo make install # install mrbayes # 2024/04/19 # 3.2.6 -> 3.2.7 chkuo@koa[/usr/local]$ sudo wget https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/mrbayes-3.2.7.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf mrbayes-3.2.7.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root mrbayes-3.2.7 chkuo@koa[/usr/local]$ cd mrbayes-3.2.7 chkuo@koa[/usr/local/mrbayes-3.2.7]$ sudo ./configure --with-mpi chkuo@koa[/usr/local/mrbayes-3.2.7]$ sudo make chkuo@koa[/usr/local/mrbayes-3.2.7]$ sudo make install chkuo@koa[/usr/local/mrbayes-3.2.7]$ /usr/local/bin/mb -v Version: 3.2.7
chkuo@cherry[/usr/local]$ sudo git clone git://github.com/indraniel/sff2fastq.git chkuo@cherry[/usr/local]$ cd sff2fastq/ chkuo@cherry[/usr/local/sff2fastq]$ sudo make chkuo@cherry[/usr/local/sff2fastq]$ sudo ln -s /usr/local/sff2fastq/sff2fastq /usr/local/bin/sff2fastq
chkuo@koa[/usr/local]$ sudo apt install fastx-toolkit
# prepare files chkuo@koa[/usr/local/phred_020425]$ sudo uncompress phred-dist-020425.c-acd.tar.Z chkuo@koa[/usr/local/phred_020425]$ sudo tar -xvf phred-dist-020425.c-acd.tar # change ownership chkuo@koa[/usr/local/phred_020425]$ sudo chown root:root * # edit Makefile # uncomment 'LXFLAGS= -DX86_GCC_LINUX' (line 8) chkuo@koa[/usr/local/phred_020425]$ sudo emacs Makefile # compile phred chkuo@koa[/usr/local/phred_020425]$ sudo make # compile daev chkuo@koa[/usr/local/phred_020425]$ sudo make daev # clean up chkuo@koa[/usr/local/phred_020425]$ sudo rm *.o # remove read permission according to the academic user agreement chkuo@koa[/usr/local/phred_020425]$ sudo chmod go-r * # add read permission for .DOC files chkuo@koa[/usr/local/phred_020425]$ sudo chmod a+r *.DOC # add read permission for phredpar.dat chkuo@koa[/usr/local/phred_020425]$ sudo chmod a+r phredpar.dat # edit the phredpar.dat # the sequencing core at IPMB uses ABI 3730 # need to append the following lines to # /usr/local/phred/phredpar.dat # # "KB_3730_POP7_BDTv1.mob" terminator big-dye ABI_3700 # "KB_3730_POP7_BDTv3.mob" terminator big-dye ABI_3700 # # note: ABI 3730 is not recognized, use 3700 as the substitute chkuo@koa[/usr/local/phred_020425]$ sudo emacs phredpar.dat # create symbolic links chkuo@koa[~]$ sudo ln -s /usr/local/phred_020425 /usr/local/phred chkuo@koa[~]$ sudo ln -s /usr/local/phred/phred /usr/local/bin/phred chkuo@koa[~]$ sudo ln -s /usr/local/phred/daev /usr/local/bin/daev # set the 'PHRED_PARAMETER_FILE' environment variable chkuo@koa[~]$ sudo emacs /etc/environment # verify the setting chkuo@koa[~]$ grep PHRED_PARAMETER_FILE /etc/environment PHRED_PARAMETER_FILE="/usr/local/phred/phredpar.dat"
# prepare files chkuo@koa[/usr/local/phd2fasta]$ sudo uncompress phd2fasta-acd-dist.tar.Z chkuo@koa[/usr/local/phd2fasta]$ sudo tar -xvf phd2fasta-acd-dist.tar # change ownership chkuo@koa[/usr/local/phd2fasta]$ sudo chown root:root * # compile chkuo@koa[/usr/local/phd2fasta]$ sudo make # clean up chkuo@koa[/usr/local/phd2fasta]$ sudo rm *.o # remove read permission according to the academic user agreement chkuo@koa[/usr/local/phd2fasta]$ sudo chmod go-r * # add read permission for .DOC files chkuo@koa[/usr/local/phd2fasta]$ sudo chmod a+r *.DOC # create symbolic links chkuo@koa[~]$ sudo ln -s /usr/local/phd2fasta/phd2fasta /usr/local/bin/phd2fasta
# prepare files chkuo@koa[/usr/local/phrap]$ sudo tar -xzvf distrib.tar.gz # change ownership chkuo@koa[/usr/local/phrap]$ sudo chown -R root:root * # compile chkuo@koa[/usr/local/phrap]$ sudo make # clean up chkuo@koa[/usr/local/phrap]$ sudo rm *.o # remove read permission according to the academic user agreement chkuo@koa[/usr/local/phrap]$ sudo chmod go-r * # add read permission for .doc files chkuo@koa[/usr/local/phrap]$ sudo chmod a+r *.doc # create symbolic links chkuo@koa[~]$ sudo ln -s /usr/local/phrap/phrap /usr/local/bin/phrap chkuo@koa[~]$ sudo ln -s /usr/local/phrap/cross_match /usr/local/bin/cross_match chkuo@koa[~]$ sudo ln -s /usr/local/phrap/swat /usr/local/bin/swat chkuo@koa[~]$ sudo ln -s /usr/local/phrap/phrapview /usr/local/bin/phrapview
# Installing chkuo@koa[/usr/local/consed]$ sudo tar -xzvf consed_linux.tar.gz chkuo@koa[/usr/local/consed]$ sudo chown -R root:root * chkuo@koa[/usr/local/consed]$ sudo chmod go-r * chkuo@koa[/usr/local/consed]$ sudo chmod a+r *txt
chkuo@koa[/usr/local]$ sudo wget http://downloads.sourceforge.net/project/lucy/lucy/lucy%201.20/lucy1.20.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf lucy1.20.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root lucy-1.20p/ chkuo@koa[/usr/local/lucy-1.20p]$ sudo make chkuo@koa[/usr/local]$ sudo ln -s /usr/local/lucy-1.20p/lucy /usr/local/bin/lucy
chkuo@cherry[/usr/local]$ sudo wget http://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.10.1.zip chkuo@cherry[/usr/local]$ sudo unzip rdp_classifier_2.10.1.zip chkuo@cherry[/usr/local]$ sudo rm /usr/local/rdp_classifier_2.10.1.zip
chkuo@koa[/usr/local]$ sudo wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip chkuo@koa[/usr/local]$ sudo unzip fastqc_v0.11.8.zip chkuo@koa[/usr/local]$ sudo chmod a+x FastQC/fastqc
chkuo@koa[/usr/local]$ sudo wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip chkuo@koa[/usr/local]$ sudo unzip Trimmomatic-0.39.zip chkuo@koa[/usr/local]$ sudo chmod 755 /usr/local/Trimmomatic-0.39/trimmomatic-0.39.jar
chuan@koa:/usr/local$ sudo wget https://sourceforge.net/projects/bbmap/files/BBMap_38.73.tar.gz chuan@koa:/usr/local$ sudo tar xzf BBMap_38.73.tar.gz chuan@koa:/usr/local$ sudo ln -s /usr/local/bbmap /usr/local/bin/bbmap chuan@koa:/usr/local$ sudo chmod 755 bbmap/* chuan@koa:/usr/local$ sudo ln -s /usr/local/bbmap/stats.sh /usr/local/bin/stats.sh
chuan@koa:/usr/local$ sudo wget -N http://www.bnxinstall.com/access/tools/access.tools.tgz chuan@koa:/usr/local$ sudo tar -xvf access.tools.tgz chuan@koa:/usr/local$ sudo apt-get install yum chuan@koa:/usr/local$ sudo python tools/access/1.0/pbng-install.chuan.py tools/access/1.0/bng-install.chuan.sh koa
chkuo@koa[/usr/local]$ sudo wget http://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz chkuo@koa[/usr/local]$ sudo tar -xzvf FLASH-1.2.11.tar.gz chkuo@koa[/usr/local]$ cd FLASH-1.2.11/ chkuo@koa[/usr/local/FLASH-1.2.11]$ sudo make chkuo@koa[/usr/local/FLASH-1.2.11]$ sudo ln -s /usr/local/FLASH-1.2.11/flash /usr/local/bin/flash
chkuo@koa[/usr/local]$ sudo wget http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 chkuo@koa[/usr/local]$ sudo tar -jxvf bwa-0.7.17.tar.bz2 chkuo@koa[/usr/local]$ sudo chown -R root:root bwa-0.7.17 chkuo@koa[/usr/local]$ cd bwa-0.7.17 chkuo@koa[/usr/local/bwa-0.7.17]$ sudo make chkuo@koa[/usr/local/bwa-0.7.17]$ sudo ln -s /usr/local/bwa-0.7.17/bwa /usr/local/bin/bwa chkuo@koa[/usr/local/bwa-0.7.17]$ which bwa /usr/local/bin/bwa
# prerequisite: Threading Building Blocks library (TBB) chkuo@koa[/usr/local]$ sudo apt-cache search tbb chkuo@koa[/usr/local]$ sudo apt install libtbb-dev # install chkuo@koa[/usr/local]$ sudo wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.3/bowtie2-2.3.4.3-source.zip chkuo@koa[/usr/local]$ sudo unzip bowtie2-2.3.4.3-source.zip chkuo@koa[/usr/local]$ cd bowtie2-2.3.4.3 chkuo@koa[/usr/local/bowtie2-2.3.4.3]$ sudo make chkuo@koa[/usr/local/bowtie2-2.3.4.3]$ sudo ln -s /usr/local/bowtie2-2.3.4.3/bowtie2 /usr/local/bin/bowtie2 chkuo@koa[/usr/local/bowtie2-2.3.4.3]$ sudo ln -s /usr/local/bowtie2-2.3.4.3/bowtie2-build /usr/local/bin/bowtie2-build
chkuo@cherry[/usr/local]$ sudo wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz chkuo@cherry[/usr/local]$ sudo tar -xzvf tophat-2.0.13.Linux_x86_64.tar.gz chkuo@cherry[/usr/local]$ sudo chown -R root:root tophat-2.0.13.Linux_x86_64 chkuo@cherry[/usr/local]$ sudo ln -s /usr/local/tophat-2.0.13.Linux_x86_64/tophat /usr/local/bin/tophat chkuo@cherry[/usr/local]$ sudo rm /usr/local/tophat-2.0.13.Linux_x86_64.tar.gz
chkuo@koa[/usr/local]$ sudo curl -L https://github.com/lh3/minimap2/releases/download/v2.15/minimap2-2.15_x64-linux.tar.bz2 | sudo tar -jxvf - chkuo@koa[/usr/local]$ sudo chown -R root:root minimap2-2.15_x64-linux chkuo@koa[/usr/local]$ sudo ln -s /usr/local/minimap2-2.15_x64-linux/minimap2 /usr/local/bin/minimap2
chkuo@cherry[/usr/local]$ sudo wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz chkuo@cherry[/usr/local]$ sudo tar -xzvf cufflinks-2.2.1.Linux_x86_64.tar.gz chkuo@cherry[/usr/local]$ sudo chown -R root:root cufflinks-2.2.1.Linux_x86_64 chkuo@cherry[/usr/local]$ sudo ln -s /usr/local/cufflinks-2.2.1.Linux_x86_64/cufflinks /usr/local/bin/cufflinks chkuo@cherry[/usr/local]$ sudo ln -s /usr/local/cufflinks-2.2.1.Linux_x86_64/cuffdiff /usr/local/bin/cuffdiff chkuo@cherry[/usr/local]$ sudo ln -s /usr/local/cufflinks-2.2.1.Linux_x86_64/cuffcompare /usr/local/bin/cuffcompare chkuo@cherry[/usr/local]$ sudo rm /usr/local/cufflinks-2.2.1.Linux_x86_64.tar.gz
chkuo@koa[/usr/local]$ sudo wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 chkuo@koa[/usr/local]$ sudo tar -jxvf samtools-1.9.tar.bz2 chkuo@koa[/usr/local]$ cd samtools-1.9 chkuo@koa[/usr/local/samtools-1.9]$ sudo make chkuo@koa[/usr/local/samtools-1.9]$ sudo make install
chkuo@koa[/usr/local]$ sudo wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 chkuo@koa[/usr/local]$ sudo tar -jxvf bcftools-1.9.tar.bz2 chkuo@koa[/usr/local]$ cd bcftools-1.9 chkuo@koa[/usr/local/bcftools-1.9]$ sudo make chkuo@koa[/usr/local/bcftools-1.9]$ sudo make install
chkuo@koa[/usr/local]$ sudo wget https://github.com/broadinstitute/picard/archive/2.18.20.tar.gz chkuo@koa[/usr/local]$ sudo tar -xzvf 2.18.20.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root picard-2.18.20
hychang@koa:[~]$ sudo apt install python3-htseq # [sudo] password for hychang: # Reading package lists... Done # Building dependency tree # Reading state information... Done # E: Unable to locate package python3-htseq hychang@koa:[~]$ htseq-count --version # 2.0.2 hychang@koa:[~]$ whereis htseq-count # htseq-count: /usr/local/bin/htseq-count
# requires python-dev chkuo@cherry[/usr/local]$ sudo apt-get install python-dev # setuptools is required for nose chkuo@cherry[/usr/local]$ sudo wget http://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11-py2.7.egg chkuo@cherry[/usr/local]$ sudo sh setuptools-0.6c11-py2.7.egg # nose is required for screed # screed is required for khmer chkuo@cherry[/usr/local]$ sudo /usr/local/bin/easy_install nose chkuo@cherry[/usr/local]$ sudo /usr/local/bin/easy_install virtualenv chkuo@cherry[/usr/local]$ sudo python -m virtualenv env chkuo@cherry[/usr/local]$ sudo chmod a+x ./env/bin/activate* chkuo@cherry[/usr/local]$ source ./env/bin/activate chkuo@cherry[/usr/local]$ sudo git clone git://github.com/ctb/screed.git chkuo@cherry[/usr/local]$ sudo /usr/local/bin/easy_install screed chkuo@cherry[/usr/local]$ sudo git clone git://github.com/ctb/khmer.git chkuo@cherry[/usr/local/khmer]$ sudo make clean all chkuo@cherry[/usr/local/khmer]$ sudo easy_install nose chkuo@cherry[/usr/local/khmer]$ sudo make test chkuo@cherry[/usr/local]$ sudo /usr/local/bin/easy_install /usr/local/khmer
chkuo@cherry[/usr/local]$ sudo wget http://kmergenie.bx.psu.edu/kmergenie-1.6950.tar.gz chkuo@cherry[/usr/local]$ sudo tar -xzvf kmergenie-1.6950.tar.gz chkuo@cherry[/usr/local]$ sudo chown -R root:root kmergenie-1.6950 chkuo@cherry[/usr/local]$ cd kmergenie-1.6950 chkuo@cherry[/usr/local/kmergenie-1.6950]$ sudo make clean chkuo@cherry[/usr/local/kmergenie-1.6950]$ sudo make k=200 chkuo@cherry[/usr/local]$ sudo rm /usr/local/kmergenie-1.6950.tar.gz
chkuo@koa[/usr/local]$ sudo wget http://cab.spbu.ru/files/release3.15.0/SPAdes-3.15.0-Linux.tar.gz chkuo@koa[/usr/local]$ sudo tar -xzf SPAdes-3.15.0-Linux.tar.gz chkuo@koa[/usr/local]$ sudo ln -s /usr/local/SPAdes-3.15.0-Linux/bin/spades.py /usr/local/bin/spades.py
chuan@koa:/usr/local$ sudo wget -O supernova-2.1.1.tar.gz "http://cf.10xgenomics.com/releases/assembly/supernova-2.1.1.tar.gz?Expires=1574703423&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9hc3NlbWJseS9zdXBlcm5vdmEtMi4xLjEudGFyLmd6IiwiQ29uZGl0aW9uIjp7IkRhdGVMZXNzVGhhbiI6eyJBV1M6RXBvY2hUaW1lIjoxNTc0NzAzNDIzfX19XX0_&Signature=kbsBuCSa6ADfZycv8U1Onc7N3Sz1w0-gZViJRfJp7HClpJTLD-SjzcYvjw-6wR9yDX1KswanWLEOhx48b-6rgh44p73-t547E7esV2XIVgHjjWTlSM4KzHmvhu6j4mtDf~rj5tlM1fGfh-53SvZvNofGwElJo97VPbB-LDutDZp0lfrcDwU1vjizKCXLOlRFKmrR9x6-Njss0J7YFmOhgGqm32kzoffP9plLzV30O1~WGc0M5n8~ENTvvqgz3ACcv7Ue1KvR8ycN0vlNAmafKiNtt5tJvcSFD35xVreqC9ii22LoJHwbFxcC9X8PR24lmylpAt6yYcD1M7vn57krRw__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA" chuan@koa:/usr/local$ sudo tar -xzf supernova-2.1.1.tar.gz chuan@koa:/usr/local$ sudo ln -s /usr/local/supernova-2.1.1/supernova /usr/local/bin/supernova
chuan@koa:/usr/local$ sudo wget -O longranger-2.2.2.tar.gz "http://cf.10xgenomics.com/releases/genome/longranger-2.2.2.tar.gz?Expires=1584541789&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9nZW5vbWUvbG9uZ3Jhbmdlci0yLjIuMi50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE1ODQ1NDE3ODl9fX1dfQ__&Signature=iUgYd~EJ5iVwEHFyUhBBMkJrfgDV0Ltnx28U7~eM9FpNFun4qG~3DEpl9XXrIeYPYJDlLcmvuusq6TUtCFxQaTP1AgA-rXUeEYt6p~IDUmr0j7V026cxh2sKfuYb4qLOeBaYwmCw9n6rjR1tXKremhPBttJX65Ar6T~xhzj9zBi3F3ELBJupKiHmVKOqW0RtkM2U8KMXMxFUmSH5JRLOoh3hG5~bg9-wzH-4uVH1fIccXnNlqzV4Nqw4yJZbaNZIhgqsmt64LX1MJ1fC1Z-HrwbOyrSjyTl62j3yBMCbW~S5DvQTd3P~1uToCqgyEoRueALpS6aKVD6eLBKpGe0p9A__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA" chuan@koa:/usr/local$ sudo tar -xzf longranger-2.2.2.tar.gz chuan@koa:/usr/local$ sudo ln -s /usr/local/longranger-2.2.2/longranger /usr/local/bin/longranger # 4792320 barcodes on the whitelist: /usr/local/longranger-2.2.2/longranger-cs/2.2.2/tenkit/lib/python/tenkit/barcodes/4M-with-alts-february-2016.txt
chuan@koa:/usr/local$ sudo wget https://github.com/bcgsc/arcs/archive/master.zip chuan@koa:/usr/local$ sudo unzip master.zip chuan@koa:/usr/local$ sudo mv arcs-master arcs-1.1.1 chuan@koa:/usr/local$ cd arcs-1.1.1/ chuan@koa:/usr/local/arcs-1.1.1$ sudo ./autogen.sh chuan@koa:/usr/local/arcs-1.1.1$ sudo wget https://sourceforge.net/projects/boost/files/boost/1.58.0/boost_1_58_0.tar.bz2 chuan@koa:/usr/local/arcs-1.1.1$ sudo tar jxf boost_1_58_0.tar.bz2 chuan@koa:/usr/local/arcs-1.1.1$ sudo ./configure –-with-boost=/usr/local/arcs-1.1.1/boost_1_58_0 chuan@koa:/usr/local/arcs-1.1.1$ sudo apt-get install libsparsehash-dev # dependency: google/sparse_hash_map chuan@koa:/usr/local/arcs-1.1.1$ sudo make chuan@koa:/usr/local/arcs-1.1.1$ sudo ln -s /usr/local/arcs-1.1.1/Arcs/arcs /usr/local/bin/arcs # dependency: LINKS chuan@koa:/usr/local$ sudo wget https://github.com/bcgsc/LINKS/releases/download/v1.8.7/links_v1-8-7.tar.gz chuan@koa:/usr/local$ sudo tar -xvf links_v1-8-7.tar.gz chuan@koa:/usr/local$ sudo ln -s /usr/local/links_v1.8.7/LINKS /usr/local/bin/LINKS
chkuo@koa[/usr/local]$ sudo wget http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz chkuo@koa[/usr/local]$ sudo tar xzf velvet_1.2.10.tgz chkuo@koa[/usr/local]$ sudo chown -R root:root velvet_1.2.10 chkuo@koa[/usr/local]$ sudo chmod 755 velvet_1.2.10 chkuo@koa[/usr/local]$ cd velvet_1.2.10 chkuo@koa[/usr/local/velvet_1.2.10]$ sudo make 'CATEGORIES=10' 'MAXKMERLENGTH=301' 'LONGSEQUENCES=1' 'OPENMP=1' chkuo@koa[/usr/local/bin]$ sudo ln -s /usr/local/velvet_1.2.10/velvetg /usr/local/bin/velvetg chkuo@koa[/usr/local/bin]$ sudo ln -s /usr/local/velvet_1.2.10/velveth /usr/local/bin/velveth
chkuo@koa[/usr/local]$ sudo wget http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf VelvetOptimiser-2.2.5.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root VelvetOptimiser-2.2.5 chkuo@koa[/usr/local]$ sudo chmod 755 VelvetOptimiser-2.2.5
chkuo@koa[/usr/local]$ sudo wget http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz chkuo@koa[/usr/local]$ sudo tar xzf oases_0.2.08.tgz chkuo@koa[/usr/local]$ sudo chown -R root:root oases_0.2.8 chkuo@koa[/usr/local]$ sudo chmod 755 oases_0.2.8 chkuo@koa[/usr/local]$ cd oases_0.2.8 chkuo@koa[/usr/local/oases_0.2.8]$ sudo make 'VELVET_DIR=/usr/local/velvet_1.2.10' 'CATEGORIES=10' 'MAXKMERLENGTH=301' chkuo@koa[/usr/local/bin]$ sudo ln -s /usr/local/oases_0.2.8/oases /usr/local/bin/oases
# 2023/09/07; v0.4.9b -> v0.5.0; chkuo # 2020/04/29; v0.4.8b -> v0.4.9b; chkuo chkuo@koa[/usr/local]$ sudo git clone https://github.com/rrwick/Unicycler.git chkuo@koa[/usr/local]$ sudo mv Unicycler unicycler-0.5.0 chkuo@koa[/usr/local]$ cd unicycler-0.5.0 chkuo@koa[/usr/local/unicycler-0.5.0]$ sudo python3 setup.py install chkuo@koa[/usr/local/unicycler-0.5.0]$ unicycler --version Unicycler v0.5.0
# prerequisites (note the order) # GMP (https://gmplib.org/) chkuo@koa[/usr/local]$ sudo apt install libgmp-dev # MPFR (https://www.mpfr.org/) chkuo@koa[/usr/local]$ sudo apt install libmpfr-dev # MPC (http://www.multiprecision.org/mpc/) chkuo@koa[/usr/local]$ sudo apt install libmpc-dev # Picard (http://picard.sourceforge.net/); installed already # graphviz (http://www.graphviz.org/) chkuo@koa[/usr/local]$ sudo apt install graphviz # g++ (v4.7.0 or higher according to AllPaths-LG manual # IMPORTANT: # Ubuntu 18.04 comes with gcc v7.3.0 # use v7.3.0 causes "make" to fail with these error messages # # Makefile:2654: recipe for target 'CleanEfasta.o' failed # make[1]: *** [CleanEfasta.o] Error 1 # make[1]: Leaving directory '/usr/local/allpathslg-52488/src' # Makefile:284: recipe for target 'all-recursive' failed # make: *** [all-recursive] Error 1 # # install g++ v4.8 and use this version in the "./configure" step (see below; CXX/CXXPP options) chkuo@koa[/usr/local]$ sudo apt install g++-4.8 # libieee # IMPORTANT: # Ubuntu 18.04 uses glibc v2.27 # which does not support libieee and causes "make" to fail with these error messages # # /usr/bin/ld: cannot find -lieee # collect2: error: ld returned 1 exit status # Makefile:2096: recipe for target 'RemodelGaps' failed # make[1]: *** [RemodelGaps] Error 1 # make[1]: Leaving directory '/usr/local/allpathslg-52188/src' # Makefile:284: recipe for target 'all-recursive' failed # make: *** [all-recursive] Error 1 # # install libieee1284-3 and create a symbolic link chkuo@koa[/usr/local]$ sudo apt install libieee1284-3 chkuo@koa[/usr/local]$ sudo ln -s /usr/lib/x86_64-linux-gnu/libieee1284.so.3 /usr/lib/libieee.so # # start AllPaths-LG installation chkuo@koa[/usr/local]$ sudo wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/allpathslg-52488.tar.gz chkuo@koa[/usr/local]$ sudo tar xzf allpathslg-52488.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root allpathslg-52488 chkuo@koa[/usr/local]$ sudo chmod 755 allpathslg-52488 chkuo@koa[/usr/local]$ cd allpathslg-52488 chkuo@koa[/usr/local/allpathslg-52488]$ sudo ./configure --prefix=/usr/local CXX=/usr/bin/g++-4.8 CXXPP=/usr/bin/cpp-4.8 chkuo@koa[/usr/local/allpathslg-52488]$ sudo make chkuo@koa[/usr/local/allpathslg-52488]$ sudo make install
chkuo@cherry[/usr/local]$ sudo wget http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/mira_4.0rc5_linux-gnu_x86_64_static.tar.bz2 chkuo@cherry[/usr/local]$ sudo tar -jxvf mira_4.0rc5_linux-gnu_x86_64_static.tar.bz2 chkuo@cherry[/usr/local]$ sudo chown -R root:root mira_4.0rc5_linux-gnu_x86_64_static chkuo@cherry[/usr/local]$ sudo chmod 755 mira_4.0rc5_linux-gnu_x86_64_static chkuo@cherry[/usr/local]$ sudo ln -s /usr/local/mira_4.0rc5_linux-gnu_x86_64_static/bin/mira /usr/local/bin/mira chkuo@cherry[/usr/local]$ sudo rm mira_4.0rc5_linux-gnu_x86_64_static.tar.bz2
chkuo@cherry[/usr/local]$ sudo wget http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.1/wgs-8.1-Linux-amd64.tar.bz2 chkuo@cherry[/usr/local]$ sudo tar -jxvf wgs-8.1-Linux-amd64.tar.bz2 chkuo@cherry[/usr/local]$ sudo chown -R root:root wgs-8.1 chkuo@cherry[/usr/local]$ sudo chmod 755 wgs-8.1 chkuo@cherry[/usr/local]$ sudo rm wgs-8.1-Linux-amd64.tar.bz2
# Software Requirement # MySQL 5 (apt-get install mysql-server) # Perl (v5.10.1) Statistics::Descriptive Perl module: sudo cpan Statistics::Descriptive # create 'smrtanalysis' user with sudo privileges (add to 'adm' and 'sudo' group) smrtanalysis@cherry[/opt]$ sudo wget http://files.pacb.com/software/smrtanalysis/2.1.1/smrtanalysis-2.1.1-ubuntu-12.04.run smrtanalysis@cherry[/opt]$ sudo chown smrtanalysis:smrtanalysis smrtanalysis-2.1.1-ubuntu-12.04.run smrtanalysis@cherry[/opt]$ SMRT_ROOT=/opt/smrtanalysis smrtanalysis@cherry[/opt]$ sudo mkdir $SMRT_ROOT smrtanalysis@cherry[/opt]$ sudo chown smrtanalysis:smrtanalysis $SMRT_ROOT smrtanalysis@cherry[/opt]$ bash smrtanalysis-2.1.1-ubuntu-12.04.run --rootdir $SMRT_ROOT # requires remote access by SMRT Portal, abort installation
chkuo@cherry[/usr/local]$ sudo wget http://sourceforge.net/projects/amos/files/amos/3.1.0/amos-3.1.0.tar.gz chkuo@cherry[/usr/local]$ sudo tar xzf amos-3.1.0.tar.gz chkuo@cherry[/usr/local]$ sudo chown -R root:root amos-3.1.0 chkuo@cherry[/usr/local]$ sudo chmod 755 amos-3.1.0 chkuo@cherry[/usr/local]$ cd amos-3.1.0/ chkuo@cherry[/usr/local/amos-3.1.0]$ sudo aptitude install ash coreutils gawk gcc automake libboost-dev chkuo@cherry[/usr/local/amos-3.1.0]$ sudo apt-get install libqt4-core chkuo@cherry[/usr/local/amos-3.1.0]$ sudo apt-get install libqt4-dev # http://seqanswers.com/forums/showthread.php?t=17802 # edit 'src/Align/find-tandem.cc' # add '#include <getopt.h>' chkuo@cherry[/usr/local/amos-3.1.0]$ sudo ./configure chkuo@cherry[/usr/local/amos-3.1.0]$ sudo make chkuo@cherry[/usr/local/amos-3.1.0]$ sudo make check chkuo@cherry[/usr/local/amos-3.1.0]$ sudo make install chkuo@cherry[/usr/local/amos-3.1.0]$ sudo ln -s /usr/local/amos-3.1.0/bin/* /usr/local/bin/
chkuo@cherry[/usr/local]$ sudo wget ftp://ftp.sanger.ac.uk/pub4/resources/software/phusion/phusion_pipeline_v2.1c.tar.gz chkuo@cherry[/usr/local]$ sudo tar -xzvf phusion_pipeline_v2.1c.tar.gz # note: need to install tcsh first chkuo@cherry[/usr/local/phusion_pipeline_v2.1c]$ sudo ./install.csh
chuan@koa[/usr/local]$ sudo wget https://github.com/alekseyzimin/masurca/releases/download/v4.0.3/MaSuRCA-4.0.3.tar.gz chuan@koa[/usr/local]$ sudo tar xzf MaSuRCA-4.0.3.tar.gz chuan@koa[/usr/local]$ cd MaSuRCA-4.0.3 chuan@koa[/usr/local/MaSuRCA-4.0.3]$ sudo BOOST_ROOT=install ./install.sh
chkuo@koa[/usr/local]$ sudo git clone --recursive https://github.com/isovic/racon.git racon chkuo@koa[/usr/local]$ cd racon chkuo@koa[/usr/local/racon]$ sudo mkdir build chkuo@koa[/usr/local/racon]$ cd build chkuo@koa[/usr/local/racon/build]$ sudo cmake -DCMAKE_BUILD_TYPE=Release .. chkuo@koa[/usr/local/racon/build]$ sudo make chkuo@koa[/usr/local/racon/build]$ sudo ln -s /usr/local/racon/build/bin/racon /usr/local/bin/racon
chuan@koa[/usr/local]$ sudo git clone https://github.com/lbcb-sci/raven chuan@koa[/usr/local]$ cd raven chuan@koa[/usr/local/raven]$ sudo mkdir build chuan@koa[/usr/local/raven]$ cd build chuan@koa[/usr/local/raven/build]$ sudo cmake -DCMAKE_BUILD_TYPE=Release .. chuan@koa[/usr/local/raven/build]$ sudo make chkuo@koa[/usr/local/raven/build]$ sudo ln -s /usr/local/raven/build/bin/raven /usr/local/bin/raven
chuan@koa[/usr/local]$ sudo wget https://github.com/Nextomics/NextPolish/releases/download/v1.3.1/NextPolish.tgz chuan@koa[/usr/local]$ sudo tar -xzf NextPolish.tgz && cd NextPolish && make
chuan@koa[/usr/local]$ sudo wget https://github.com/Nextomics/NextDenovo/releases/download/v2.4.0/NextDenovo.tgz chuan@koa[/usr/local]$ sudo tar -xzf NextDenovo.tgz && cd NextDenovo
chkuo@koa[/usr/local/bin]$ sudo wget https://github.com/broadinstitute/pilon/releases/download/v1.23/pilon-1.23.jar chkuo@koa[/usr/local/bin]$ sudo chmod 755 pilon-1.23.jar
chkuo@koa[/usr/local/PAGIT.V1.01]$ sudo wget ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V1.01.64bit.tgz chkuo@koa[/usr/local/PAGIT.V1.01]$ sudo tar xzf PAGIT.V1.64bit.tgz chkuo@koa[/usr/local/PAGIT.V1.01]$ sudo chown -R root:root * chkuo@koa[/usr/local/PAGIT.V1.01]$ sudo ./installme.sh chkuo@koa[/usr/local/PAGIT.V1.01]$ sudo rm PAGIT.V1.64bit.tgz
chkuo@cherry[/usr/local]$ sudo wget http://www.cbcb.umd.edu/finishing/soma-v2.tar.gz chkuo@cherry[/usr/local]$ sudo tar xzf soma-v2.tar.gz chkuo@cherry[/usr/local]$ sudo chown -R root:root soma-v2 chkuo@cherry[/usr/local]$ sudo chmod 755 soma-v2 chkuo@cherry[/usr/local]$ sudo ln -s soma-v2 soma chkuo@cherry[/usr/local/soma/src]$ sudo make install chkuo@cherry[/usr/local/soma/bin]$ sudo chmod a+x *.pl chkuo@cherry[/usr/local]$ sudo rm /usr/local/soma-v2.tar.gz
# 2021/09/27; chkuo chkuo@koa[/usr/local]$ sudo wget https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip chkuo@koa[/usr/local]$ sudo unzip pplacer-linux-v1.1.alpha19.zip chkuo@koa[/usr/local]$ sudo chown -R root:root pplacer-* chkuo@koa[/usr/local]$ sudo ln -s /usr/local/pplacer-Linux-v1.1.alpha19/guppy /usr/local/bin/guppy chkuo@koa[/usr/local]$ sudo ln -s /usr/local/pplacer-Linux-v1.1.alpha19/pplacer /usr/local/bin/pplacer chkuo@koa[/usr/local]$ sudo ln -s /usr/local/pplacer-Linux-v1.1.alpha19/rppr /usr/local/bin/rppr # CheckM v1.1.3 chkuo@koa[~]$ sudo -H pip3 install numpy chkuo@koa[~]$ sudo -H pip3 install matplotlib chkuo@koa[~]$ sudo -H pip3 install pysam chkuo@koa[~]$ sudo -H pip3 install checkm-genome chkuo@koa[/usr/local/checkm]$ sudo wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz chkuo@koa[/usr/local/checkm]$ sudo tar xzvf checkm_data_2015_01_16.tar.gz chkuo@koa[~]$ sudo checkm data setRoot /usr/local/checkm chkuo@koa[~]$ checkm
chkuo@cherry[/usr/local/originx]$ sudo wget http://www.cbs.dtu.dk/services/GenomeAtlas-2.0/suppl/origin/originx.source.tar.gz chkuo@cherry[/usr/local/originx]$ sudo tar -xzvf originx.source.tar.gz chkuo@cherry[/usr/local/originx]$ sudo chown -R root:root * chkuo@cherry[/usr/local/originx/src]$ sudo make chkuo@cherry[/usr/local/originx/src]$ sudo ln -s /usr/local/originx/src/originx /usr/local/bin/originx chkuo@cherry[/usr/local/originx]$ sudo rm /usr/local//originx/originx.source.tar.gz
chkuo@koa[/usr/local]$ sudo wget http://meme-suite.org/meme-software/5.1.1/meme-5.1.1.tar.gz chkuo@koa[/usr/local]$ sudo tar -zxvf meme-5.1.1.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root meme-5.1.1 # check Perl dependencies # if something is missing, use ''sudo cpan XXX::YYY'' to install chkuo@koa[/usr/local/meme-5.1.1/scripts]$ perl dependencies.pl # configure and install chkuo@koa[/usr/local/meme-5.1.1]$ sudo ./configure --prefix=/usr/local/meme-5.1.1 --with-url=http://meme-suite.org/ --enable-build-libxml2 --enable-build-libxslt chkuo@koa[/usr/local/meme-5.1.1]$ sudo make chkuo@koa[/usr/local/meme-5.1.1]$ sudo make test chkuo@koa[/usr/local/meme-5.1.1]$ sudo make install # note # see install guide: http://meme-suite.org/doc/install.html # add this line: # ''export PATH=/usr/local/meme-5.1.1/bin:/usr/local/meme-5.1.1/libexec/meme-5.1.1:$PATH'' # to ''.profile''
# require Getopt chkuo@koa[/usr/local]$ sudo perl -e shell -MCPAN cpan>install Getopt::Std cpan>install Getopt::Long chkuo@koa[/usr/local]$ sudo apt install libperl4-corelibs-perl # chkuo@koa[/usr/local]$ sudo wget http://eddylab.org/software/hmmer/hmmer-2.3.2.tar.gz chkuo@koa[/usr/local]$ sudo tar -xzvf hmmer-2.3.2.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root hmmer-2.3.2 chkuo@koa[/usr/local]$ cd hmmer-2.3.2/ chkuo@koa[/usr/local/hmmer-2.3.2]$ sudo ./configure chkuo@koa[/usr/local/hmmer-2.3.2]$ sudo make chkuo@koa[/usr/local/hmmer-2.3.2]$ sudo make check chkuo@koa[/usr/local/hmmer-2.3.2]$ sudo make install
chuan@koa[/usr/local]$ sudo wget http://eddylab.org/software/hmmer/hmmer.tar.gz chuan@koa[/usr/local]$ sudo tar zxf hmmer.tar.gz chuan@koa[/usr/local]$ cd hmmer-3.3.2 chuan@koa[/usr/local/hmmer-3.3.2]$ sudo ./configure --prefix /usr/local/hmmer-3.3.2 chuan@koa[/usr/local/hmmer-3.3.2]$ sudo make chuan@koa[/usr/local/hmmer-3.3.2]$ sudo make check chuan@koa[/usr/local/hmmer-3.3.2]$ sudo make install
chkuo@koa[/usr/local/rnammer-1.2]$ sudo uncompress rnammer-1.2.src.tar.Z chkuo@koa[/usr/local/rnammer-1.2]$ sudo tar xvf rnammer-1.2.src.tar
chkuo@koa[/usr/local]$ sudo wget http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz chkuo@koa[/usr/local]$ sudo tar -xzvf tRNAscan-SE.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root tRNAscan-SE-1.3.1 chkuo@koa[/usr/local]$ sudo chmod 755 tRNAscan-SE-1.3.1 chkuo@koa[/usr/local]$ cd tRNAscan-SE-1.3.1 # edit Makefile # BINDIR = /usr/local/bin # LIBDIR = /usr/local/lib/tRNAscan-SE # MANDIR = /usr/local/man chkuo@koa[/usr/local/tRNAscan-SE-1.3.1]$ sudo emacs Makefile chkuo@koa[/usr/local/tRNAscan-SE-1.3.1]$ sudo make chkuo@koa[/usr/local/tRNAscan-SE-1.3.1]$ sudo make install chkuo@koa[/usr/local/tRNAscan-SE-1.3.1]$ sudo make testrun chkuo@koa[/usr/local/tRNAscan-SE-1.3.1]$ sudo make cleanup # fix permission chkuo@koa[/usr/local]$ sudo chmod 755 /usr/local/bin/tRNAscanSE # fix error: "Can't locate tRNAscanSE/Utils.pm in @INC" # add 'use lib "/usr/local/bin";' to '/usr/local/bin/tRNAscan-SE' (insert at line 28) # # alternative solution for individual users: # add the following line to .bashrc # export PERL5LIB="${PERL5LIB}:/usr/local/bin"
chkuo@koa[/usr/local]$ sudo git clone git://github.com/hyattpd/Prodigal.git chkuo@koa[/usr/local]$ cd Prodigal/ chkuo@koa[/usr/local/Prodigal]$ sudo make chkuo@koa[/usr/local/Prodigal]$ sudo ln -s /usr/local/Prodigal/prodigal /usr/local/bin/prodigal chkuo@koa[/usr/local/Prodigal]$ prodigal -v Prodigal V2.6.3: February, 2016
chuan@koa[~]$ sudo apt install augustus augustus-data augustus-doc # run augustus chuan@koa[~]$ augustus #chuan@koa[/usr/local]$ sudo git clone https://github.com/Gaius-Augustus/Augustus.git #chuan@koa[/usr/local]$ cd Augustus #chuan@koa[/usr/local/Augustus]$ sudo docker build -t augustus . # append USER to docker #chuan@koa[/usr/local/Augustus]$ sudo usermod -a -G docker USER # run augustus #chuan@koa[/usr/local/Augustus]$ sudo docker run augustus /root/augustus/bin/augustus
chkuo@koa[/usr/local]$ sudo tar -xzvf tmhmm-2.0c.Linux.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root tmhmm-2.0c chkuo@koa[/usr/local]$ sudo ln -s /usr/local/tmhmm-2.0c /usr/local/tmhmm chkuo@koa[/usr/local]$ sudo ln -s /usr/local/tmhmm/bin/decodeanhmm.Linux_x86_64 /usr/local/bin/decodeanhmm chkuo@koa[/usr/local]$ sudo ln -s /usr/local/tmhmm/bin/tmhmm /usr/local/bin/tmhmm # edit the wrapper script chkuo@koa[/usr/local]$ sudo emacs /usr/local/tmhmm/bin/tmhmm # modify the path to perl (line 1): #!/usr/bin/perl # uncomment and modify the basedir setting (line 13): # $opt_basedir = "/usr/local/tmhmm/"; # basis directory for TMHMM package
cat /scratch/chkuo/test/test.fasta | /usr/local/bin/decodeanhmm -f /usr/local/tmhmm/lib/TMHMM2.0.options -modelfile /usr/local/tmhmm/lib/TMHMM2.0.model
# 2024/02/07 # fast chkuo@koa[/usr/local]$ sudo tar -xzvf signalp-6.0h.fast.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root signalp6_fast chkuo@koa[/usr/local]$ sudo pip3 install /usr/local/signalp6_fast/signalp-6-package/ # slow chkuo@koa[/usr/local]$ sudo tar -xzvf signalp-6.0h.slow_sequential.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root signalp6_slow_sequential chkuo@koa[/usr/local]$ sudo pip3 install /usr/local/signalp6_slow_sequential/signalp-6-package/ chkuo@koa[/usr/local]$ which signalp6 /usr/local/bin/signalp6 chkuo@koa[/usr/local]$ signalp6 --version SignalP 6.0 Signal peptide prediction tool 6.0h
chkuo@koa[/usr/local]$ sudo tar -xzvf signalp-5.0.Linux.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root signalp-5.0 chkuo@koa[/usr/local]$ /usr/local/signalp-5.0/bin/signalp -version SignalP version 5.0 Linux x86_64
chkuo@koa[/usr/local]$ sudo tar -xzvf signalp-4.1c.Linux.tar.gz chkuo@koa[/usr/local]$ sudo chown -R root:root signalp-4.1 chkuo@koa[/usr/local]$ sudo ln -s /usr/local/signalp-4.1/signalp /usr/local/bin/signalp # edit the wrapper script according to the installation guide (line 13) # $ENV{SIGNALP} = '/usr/local/signalp-4.1'; chkuo@koa[/usr/local]$ sudo emacs /usr/local/bin/signalp
# SignalP v3.0 (for testing; version date: 2007/03/05; installation date: 2018/01/31) chkuo@cherry[/usr/local]$ sudo tar -xzvf signalp-3.0.Linux.tar.Z chkuo@cherry[/usr/local]$ sudo chown -R root:root signalp-3.0 # edit the wrapper script according to the installation guide (line 13) # SIGNALP=/usr/local/signalp-3.0 chkuo@cherry[/usr/local]$ sudo emacs /usr/local/bin/signalp
chkuo@koa[/usr/local/bin]$ sudo wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz chkuo@koa[/usr/local/bin]$ sudo gunzip linux64.tbl2asn.gz chkuo@koa[/usr/local/bin]$ sudo chmod 755 linux64.tbl2asn chkuo@koa[/usr/local/bin]$ sudo ln -s /usr/local/bin/linux64.tbl2asn /usr/local/bin/tbl2asn
chkuo@koa[/usr/local]$ sudo wget http://circos.ca/distribution/circos-0.69-9.tgz chkuo@koa[/usr/local]$ sudo tar -xzvf circos-0.69-9.tgz chkuo@koa[/usr/local]$ sudo chown -R root:root circos-0.69-9 # make symbolic link chkuo@koa[/usr/local]$ sudo ln -s /usr/bin/env /bin/env chkuo@koa[/usr/local]$ sudo ln -s /usr/local/circos-0.69-9/bin/circos /usr/local/bin/circos # get a list of required perl modules chkuo@koa[/usr/local]$ circos -modules # install missing modules chkuo@koa[/usr/local]$ sudo perl -MCPAN -e shell cpan[1]> install Config::General cpan[2]> install Font::TTF::Font cpan[3]> install Math::Bezier cpan[4]> install Math::Round cpan[5]> install Math::VecStat cpan[6]> install Params::Validate cpan[7]> install Regexp::Common cpan[8]> install Set::IntSpan cpan[9]> install Statistics::Basic cpan[10]> install Text::Format # check again to make sure that all tests are ok chkuo@koa[/usr/local]$ circos -modules # test man page chkuo@koa[/usr/local]$ circos -man # update setting # change "file_delim = \s" to "file_delim = \t" (line 22) chkuo@koa[/usr/local]$ sudo emacs /usr/local/circos-0.69-9/etc/housekeeping.conf # check version chkuo@koa[/usr/local]$ circos -v circos | v 0.69-8 | 15 Jun 2019 | Perl 5.026001 # note: # the version number in v0.69-9 was not updated # even though it said v0.69-8, this is truly v0.69-9 # see # https://groups.google.com/d/msg/circos-data-visualization/Yr9XOkevEq8/FWMc5w3lAQAJ
# 2024/04/02 # note: v1.34 has some error message; use v1.33 for now chkuo@koa[/usr/local/bin]$ sudo wget https://github.com/ParBLiSS/FastANI/releases/download/v1.33/fastANI-Linux64-v1.33.zip chkuo@koa[/usr/local/bin]$ sudo unzip fastANI-Linux64-v1.33.zip Archive: fastANI-Linux64-v1.33.zip inflating: fastANI chkuo@koa[/usr/local/bin]$ sudo mv fastANI fastANI_v1.33
# 2024/07/29 hychang@koa[~]$ sudo apt install parallel hychang@koa[~]$ parallel --version GNU parallel 20161222 Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015,2016 Ole Tange and Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. GNU parallel comes with no warranty. Web site: http://www.gnu.org/software/parallel When using programs that use GNU Parallel to process data for publication please cite as described in 'parallel --citation'.
# 2024/07/29 # note: hychang@koa[~]$ sudo apt install hhsuite hychang@koa[~]$ hhsearch HHsearch 3.0.0 (15-03-2015) Search a database of HMMs with a query alignment or query HMM (C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser Soding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960 (2005). Usage: hhsearch -i query -d database [options] ...