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DEPENDENCIES
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All dependecies listed below (except Linux, Python, and BioPython) may be
installed automatically by using 'bootstrap.py' provided here.
Administrators, please see the end of this document!
Required dependencies:
- Linux 64-bit (e.g. Ubuntu 12.04/14.04/16.04/18.04 or newer) with a minimum of 24 GB RAM
- Python version 2.7.x (>=2.6.0 and < 3.0 is fine)
- BioPython version 1.73 (>=1.50 is fine)
- Bowtie 64-bit version 1.2.3 <http://bowtie-bio.sourceforge.net/index.shtml>
- Bowtie2 64-bit version 2.3.5.1 <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>
- STAR version 2.7.2b <http://github.com/alexdobin/STAR/releases>
- forked SEQTK version 1.2-r101c-dirty <http://github.com/ndaniel/seqtk>
- BBMAP version 38.44 <http://sourceforge.net/projects/bbmap/>
- FASTQTK version 0.27 <http://github.com/ndaniel/fastqtk>
Optional dependencies:
- strongly recommended (expected by default to be installed but their use can
be disabled by using the command line option '--skip-blat'):
* BLAT version 0.35 <http://users.soe.ucsc.edu/~kent/src/>. Executables are
available here http://hgdownload.cse.ucsc.edu/admin/exe/ . Please, check the
license to see if it allows you to run/use it!
* faToTwoBit <http://users.soe.ucsc.edu/~kent/src/> . Executables are available
here <http://hgdownload.cse.ucsc.edu/admin/exe/>. Please, check the license to
see if it allows you to run/use it! This is needed if one plans to use BLAT.
- nice to have:
* Velvet (de novo assembler) version 1.2.10
<http://www.ebi.ac.uk/~zerbino/velvet/>. This is needed if one plans to do
de novo assembly of the reads which support the candidate fusion genes.
(required by option --assembly)
* fastq-dump version 2.9.6 from NCBI SRA Toolkit
<http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software>. This is needed if
one plans to use as input SRA files.
* Python library xlrd <http://pypi.python.org/pypi/xlrd>. This is needed in
order to parse the Excel file XLS from the ChimerDB 2.0 database.
* Python library openpyxl <http://pypi.python.org/pypi/openpyxl> . This is
needed for parsing the Excel file XLSX from the ConjoinG database.
* BWA version 0.7.12 <http://sourceforge.net/projects/bio-bwa/>
Genomic Databases (used/installed automatically by FusionCatcher):
- ENSEMBL database <http://www.ensembl.org>
- COSMIC database <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>
- TICdb database <http://www.unav.es/genetica/TICdb/>
- ChimerDB 2.0 database (literature-based annotation) <http://ercsb.ewha.ac.kr/FusionGene/index.jsp>
- ConjoinG database <http://metasystems.riken.jp/conjoing/>
- Cancer Genome Project (CGP) translocations database <http://www.sanger.ac.uk/genetics/CGP/Census/>
- CACG database <http://cgc.kribb.re.kr/map/>
- NCBI database <http://www.ncbi.nlm.nih.gov/>
- DGD database <http://dgd.genouest.org/>
- Illumina BodyMap2 RNA-seq database <http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513/>
- RNA-seq database of 95 human individuals representing 27 different tissues <http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1733/>
In cases that one wants to install FusionCatcher on a bare bone Linux machine, one can look at the following hints.
Install these before installing FusionCatcher (would make the installation smoother), for
- Ubuntu distro
```
sudo apt-get install build-essential
sudo apt-get install libncurses5-dev
sudo apt-get install gawk
sudo apt-get install gcc
sudo apt-get install g++
sudo apt-get install make
sudo apt-get install automake
sudo apt-get install gzip
sudo apt-get install bzip2
sudo apt-get install cmake
sudo apt-get install zlib1g-dev
sudo apt-get install zlib1g
sudo apt-get install wget
sudo apt-get install curl
sudo apt-get install pigz
sudo apt-get install zip
sudo apt-get install tar
sudo apt-get install unzip
sudo apt-get install libc6-dev
sudo apt-get install default-jdk
sudo apt-get install libtbb-dev
sudo apt-get install libtbb2
sudo apt-get install parallel
sudo apt-get install python
sudo apt-get install python-dev
sudo apt-get install python-numpy
sudo apt-get install python-biopython
sudo apt-get install python-xlrd
sudo apt-get install python-openpyxl
```
- RedHat/CentOS distro
```
sudo yum groupinstall "Development Tools"
sudo yum install ncurses-devel
sudo yum install awk
sudo yum install gcc
sudo yum install make
sudo yum install cmake
sudo yum install glibc-devel
sudo yum install zlib-devel
sudo yum install gzip
sudo yum install pigz
sudo yum install wget
sudo yum install curl
sudo yum install tbb-devel
sudo yum install python-devel
sudo yum install python-biopython
sudo yum install python-numpy
sudo yum install python-xlrd
sudo yum install python-openpyxl
sudo yum install java-1.8.0-openjdk* (or other Java?)
```