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Dependencies for run lncPipe Locally

Prerequisites install command (required when docker image is not favored, you should execute them via root)

  • HISAT2

      aria2c ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-Linux_x86_64.zip -q -o /opt/hisat2-2.1.0-Linux_x86_64.zip && \
  unzip -qq /opt/hisat2-2.1.0-Linux_x86_64.zip -d /opt/ && \
  rm /opt/hisat2-2.1.0-Linux_x86_64.zip && \
  cd /opt/hisat2-2.1.0 && \
  rm -rf doc example *debug MANUAL* NEWS TUTORIAL && \
  ln -s /opt/hisat2-2.1.0/hisat2* /usr/local/bin/ && \
  ln -sf /opt/hisat2-2.1.0/*.py /usr/local/bin/

  • StringTie

      aria2c http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.3b.Linux_x86_64.tar.gz -q -o /opt/stringtie-1.3.3b.Linux_x86_64.tar.gz && \
  tar xf /opt/stringtie-1.3.3b.Linux_x86_64.tar.gz --use-compress-prog=pigz -C /opt/ && \
  rm /opt/stringtie-1.3.3b.Linux_x86_64/README && \
  ln -s /opt/stringtie-1.3.3b.Linux_x86_64/stringtie /usr/local/bin/stringtie && \
  rm /opt/stringtie-1.3.3b.Linux_x86_64.tar.gz

  • gffcompare

      aria2c https://github.com/gpertea/gffcompare/archive/master.zip -q -o /opt/gffcompare-master.zip && \
  aria2c https://github.com/gpertea/gclib/archive/master.zip -q -o /opt/gclib-master.zip && \
  unzip -qq /opt/gffcompare-master.zip -d /opt/ && \
  unzip -qq /opt/gclib-master.zip -d /opt/ && \
  rm /opt/gffcompare-master.zip /opt/gclib-master.zip && \
  cd /opt/gffcompare-master && \
  make release

  • Bedops:

      aria2c https://github.com/bedops/bedops/releases/download/v2.4.29/bedops_linux_x86_64-v2.4.29.tar.bz2 -q -o /opt/bedops_linux_x86_64-v2.4.29.tar.bz2 && \
  tar xf /opt/bedops_linux_x86_64-v2.4.29.tar.bz2 --use-compress-prog=pbzip2 -C /opt/ && \
  ln -s /opt/bin/* /usr/local/bin/ && \
  rm /opt/bedops_linux_x86_64-v2.4.29.tar.bz2

  • PLEK:

      aria2c https://nchc.dl.sourceforge.net/project/plek/PLEK.1.2.tar.gz -q -o /opt/PLEK.1.2.tar.gz && \
  tar xf /opt/PLEK.1.2.tar.gz --use-compress-prog=pigz -C /opt/ && \
  cd /opt/PLEK.1.2/ && \
  python PLEK_setup.py || : && \
  rm *.pdf *.txt *.h *.c *.fa *.cpp *.o *.R *.doc PLEK_setup.py && \
  chmod 755 * && \
  perl -CD -pi -e'tr/\x{feff}//d && s/[\r\n]+/\n/' *.py && \
  ln -s /opt/PLEK.1.2/* /usr/local/bin/ && \
  rm /opt/PLEK.1.2.tar.gz

  • CNCI:

      aria2c https://codeload.github.com/www-bioinfo-org/CNCI/zip/master -q -o /opt/CNCI-master.zip && \
  unzip -qq /opt/CNCI-master.zip -d /opt/ && \
  rm /opt/CNCI-master.zip && \
  unzip -qq /opt/CNCI-master/libsvm-3.0.zip -d /opt/CNCI-master/ && \
  rm /opt/CNCI-master/libsvm-3.0.zip && \
  cd /opt/CNCI-master/libsvm-3.0 && \
  make > /dev/null 2>&1 && \
  shopt -s extglob && \
  rm -rfv !\("svm-predict"\|"svm-scale"\) && \
  cd .. && \
  rm draw_class_pie.R LICENSE README.md && \
  chmod -R 755 * && \
  ln -s /opt/CNCI-master/*.py /usr/local/bin/

  • CPAT:Citation

      aria2c https://jaist.dl.sourceforge.net/project/rna-cpat/v1.2.3/CPAT-1.2.3.tar.gz -q -o /opt/CPAT-1.2.3.tar.gz && \
  tar xf /opt/CPAT-1.2.3.tar.gz --use-compress-prog=pigz -C /opt/ && \
  cd /opt/CPAT-1.2.3/ && \
  mv dat/* /LncPipeDB/ && \
  python setup.py install > /dev/null 2>&1 && \
  rm -rf /opt/CPAT*

  • fastp

      RUN aria2c http://opengene.org/fastp/fastp -q -o /usr/local/bin/fastp && \
      chmod a+x /usr/local/bin/fastp

  • FastQC

      aria2c https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -q -o /opt/fastqc_v0.11.5.zip && \
  unzip -qq /opt/fastqc_v0.11.5.zip -d /opt/ && \
  rm /opt/fastqc_v0.11.5.zip && \
  cd /opt/FastQC && \
  shopt -s extglob && \
  rm -rfv !\("fastqc"\|*.jar\) && \
  chmod 755 * && \
  ln -s /opt/FastQC/fastqc /usr/local/bin/

  • or AfterQC

      aria2c https://github.com/OpenGene/AfterQC/archive/v0.9.7.tar.gz -q -o /opt/AfterQC-0.9.7.tar.gz && \
  tar xf /opt/AfterQC-0.9.7.tar.gz --use-compress-prog=pigz -C /opt/ && \
  cd /opt/AfterQC-0.9.7 && \
  make && \
  perl -i -lape's/python/pypy/ if $. == 1' after.py && \
  rm -rf Dockerfile Makefile README.md testdata report_sample && \
  rm editdistance/*.cpp editdistance/*.h && \
  ln -s /opt/AfterQC-0.9.7/*.py /usr/local/bin/ && \
  rm /opt/AfterQC-0.9.7.tar.gz

When using afterQC, we recommend that users install pypy in their operation system, which can accelerate about 3X speed for raw reads processing, as suggested by the author of AfterQC.

  • LncPipeReporter

      Install [pandoc](https://pandoc.org/installing.html) first. Then run commands:

  Rscript -e "install.packages('devtools'); devtools::install_github('bioinformatist/LncPipeReporter')"

  For detailed usage of LncPipeReporter in case you are going to run it separately, plz refers to [README](https://github.com/bioinformatist/LncPipeReporter#lncpipereporter) of LncPipeReporter.

  • kallisto

      aria2c https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz -q -o  /opt/kallisto_linux-v0.43.1.tar.gz && \
  tar xf /opt/kallisto_linux-v0.43.1.tar.gz --use-compress-prog=pigz -C /opt/ && \
  cd /opt && \
  rm ._* kallisto_linux-v0.43.1.tar.gz && \
  cd kallisto_linux-v0.43.1 && \
  rm -rf ._* 	README.md test && \
  ln -s /opt/kallisto_linux-v0.43.1/kallisto /usr/local/bin/

  • sambamba

      aria2c https://github.com/biod/sambamba/releases/download/v0.6.7/sambamba_v0.6.7_linux.tar.bz2 -q -o /opt/sambamba_v0.6.7_linux.tar.bz2 && \
  tar xf /opt/sambamba_v0.6.7_linux.tar.bz2 --use-compress-prog=pbzip2 -C /opt/ && \
  ln -s /opt/sambamba /usr/local/bin/ && \
  rm /opt/sambamba_v0.6.7_linux.tar.bz2

Alternatively, when you are going to using STAR-Cufflinks in your analysis, the corresponding install cmd are as follows:

  • STAR

      aria2c https://raw.githubusercontent.com/alexdobin/STAR/master/bin/Linux_x86_64/STAR -q -o /opt/STAR && \
  chmod 755 /opt/STAR && \
  ln -s /opt/STAR /usr/local/bin

  • Cufflinks

      aria2c https://github.com/bioinformatist/cufflinks/releases/download/v2.2.1/cufflinks-2.2.1.Linux_x86_64.tar.gz -q -o /opt/cufflinks-2.2.1.Linux_x86_64.tar.gz && \
  tar xf /opt/cufflinks-2.2.1.Linux_x86_64.tar.gz --use-compress-prog=pigz -C /opt/ && \
  rm /opt/cufflinks-2.2.1.Linux_x86_64/README && \
  ln -s /opt/cufflinks-2.2.1.Linux_x86_64/* /usr/local/bin/ && \
  rm /opt/cufflinks-2.2.1.Linux_x86_64.tar.gz

The gffcompare utility share the same function as cuffcompare, therefore, in STAR-cufflinks analysis pipe, gffcompare is not required.