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scallop安装脚本

2017-12-23 19:34:12830 views

scallop是最新的一款转录组组装软件,据说效果十分科学。

Github链接:https://github.com/Kingsford-Group/scallop

Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads, while also achieves both transcripts parsimony and coverage deviation minimization.

Scallop paper has been published at Nature Biotechnology. The datasets and scripts used in this paper to compare the performance of Scallop and other assemblers are available at scalloptest.

Please also checkout the podcast about Scallop (thanks Roman Cheplyaka for the interview). It is available at both the bioinformatics chat and iTunes.

下面是软件与依赖库的安装脚本:

tar zxf zlib-1.2.11.tar.gz
cd zlib-1.2.11
./configure --prefix=/home/sczhuhd/software/
make -j24
make install
cd ..

tar zxf htslib-1.6.tar.bz2
htslib-1.6
./configure --disable-bz2 --disable-lzma --disable-gcs --disable-s3 --enable-libcurl=no --prefix=/home/sczhuhd/software/
make -j24
make install
cd ..

tar jxf bcftools-1.6.tar.bz2
cd bcftools-1.6
./configure --prefix=/home/sczhuhd/software/
make -j24
make install
cd ..

tar jxf samtools-1.6.tar.bz2
cd samtools-1.6
./configure --prefix=/home/sczhuhd/software/
make -j24
make install
cd ..

tar zxf Clp.tar.gz
cd coin-Clp
./configure --prefix=/home/sczhuhd/software/
make -j24
make install
cd ..

tar zxf boost_1_65_1.tar.gz
cd boost_1_65_1
./bootstrap.sh --prefix=/home/sczhuhd/software/
./b2
cd ..

tar zxf scallop-0.10.2.tar.gz
cd scallop-0.10.2
./configure --with-htslib=/home/sczhuhd/software/ --prefix=/home/sczhuhd/software/
make -j24
make install
cd ..