diff --git a/INSTALL_from_source.md b/INSTALL_from_source.md index 606f0bc8..39adb76a 100755 --- a/INSTALL_from_source.md +++ b/INSTALL_from_source.md @@ -51,7 +51,7 @@ sudo apt-get install python3-scipy -## 1) vsearch 2.12.0 , for FROGS Preprocess and FROGS Remove_chimera +## 1) vsearch 2.15.1 , for FROGS Preprocess and FROGS Remove_chimera **require** : autoconf, zlib and bzip2 libraries @@ -63,16 +63,16 @@ sudo apt-get install autoconf libz-dev libbz2-dev ```bash cd $BIN_DIR -wget https://github.com/torognes/vsearch/archive/v2.12.0.tar.gz -tar xzf v2.12.0.tar.gz -cd vsearch-2.12.0 +wget https://github.com/torognes/vsearch/archive/v2.15.1.tar.gz +tar xzf v2.15.1.tar.gz +cd vsearch-2.15.1 ./autogen.sh ./configure make # test installation ./bin/vsearch -version # add to FROGS -ln -s $BIN_DIR/vsearch-2.12.0/bin/vsearch $FROGS_libexec/. +ln -s $BIN_DIR/vsearch-2.15.1/bin/vsearch $FROGS_libexec/. ``` ## 2) FLASH 1.2.11 (optional), for FROGS Preprocess @@ -95,9 +95,12 @@ ln -s $BIN_DIR/FLASH-1.2.11/flash $FROGS_libexec/. ask for download link and follow installation instructions -## 4) cutadpat 3.1, for FROGS Preprocess +## 4) cutadpat 2.10 , for FROGS Preprocess **require** : pip3 + +Tests have been done until cutadapt 3.1, minimum version required 2.8 + ```bash sudo apt-get install python3-pip ``` @@ -105,22 +108,22 @@ sudo apt-get install python3-pip **installation** ```bash cd $BIN_DIR -mkdir cutadapt-3.1 -cd cutadapt-3.1 +mkdir cutadapt-2.10 +cd cutadapt-2.10 # solution 1 : precise directory (not recommended if you want to use Galaxy) - sudo pip3 install --prefix=$BIN_DIR/cutadapt-3.1 cutadapt==3.1 + sudo pip3 install --prefix=$BIN_DIR/cutadapt-2.10 cutadapt==2.10 # add cutadapt python library to your PYTHONPATH echo export PYTHONPATH="$BIN_DIR/cutadapt-3.1/lib/python3.??/site-packages:\$PYTHONPATH" >> ~/.bashrc # check installation ./bin/cutadapt --version # add to FROGS - ln -s $BIN_DIR/cutadapt-3.1/bin/cutadapt $FROGS_libexec/. + ln -s $BIN_DIR/cutadapt-2.10/bin/cutadapt $FROGS_libexec/. # solution 2 let pip3 install cutadapt (binary will be available in your PATH) # in your home directory ~/.local/bin - pip3 install cutadapt==3.1 + pip3 install cutadapt==2.10 # using sudo in /usr/local/bin - sudo pip3 install cutadapt==3.1 + sudo pip3 install cutadapt==2.10 # add to FROGS link=`which cutadapt` ln -s $link $FROGS_libexec/. @@ -237,30 +240,31 @@ emboss/needleall -h ln -s $BIN_DIR/EMBOSS-6.6.0/emboss/needleall $FROGS_libexec/. ``` -## 10) MAFFT 7.475, for FROGS Tree +## 10) MAFFT 7.407, for FROGS Tree **installation** ```bash cd $BIN_DIR -wget https://mafft.cbrc.jp/alignment/software/mafft-7.475-with-extensions-src.tgz -tar -xvzf mafft-7.475-with-extensions-src.tgz -cd mafft-7.475-with-extensions +wget https://mafft.cbrc.jp/alignment/software/mafft-7.407-with-extensions-src.tgz +tar -xvzf mafft-7.407-with-extensions-src.tgz +cd mafft-7.407-with-extensions ``` Edit core/Makefile -* change `PREFIX = /usr/local` with your MAFFT directory (like `# PREFIX = /home/frogs/bin/mafft-7.475-with-extensions/` +* change `PREFIX = /usr/local` with your MAFFT directory (like `# PREFIX = /home/frogs/bin/mafft-7.407-with-extensions/` ```bash cd core make clean make make install # check installation -$BIN_DIR/mafft-7.475-with-extensions/bin/mafft -h +$BIN_DIR/mafft-7.407-with-extensions/bin/mafft -h # add to FROGS -ln -s $BIN_DIR/mafft-7.475-with-extensions/scripts/mafft $FROGS_libexec/. +ln -s $BIN_DIR/mafft-7.407-with-extensions/scripts/mafft $FROGS_libexec/. ``` -## 11) FastTree 2.1.11, for FROGS Tree +## 11) FastTree 2.1.9, for FROGS Tree **installation** + ```bash cd $BIN_DIR mkdir Fasttree @@ -317,6 +321,8 @@ library(phangorn) ``` * phyloseq (this will take some times) + + version tested until 1.30 ```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") @@ -328,6 +334,8 @@ library(phyloseq) * DESeq2 + version tested until 1.26 + ```R BiocManager::install("DESeq2") diff --git a/frogs-conda-requirements.yaml b/frogs-conda-requirements.yaml index ee2ee9e6..18921158 100644 --- a/frogs-conda-requirements.yaml +++ b/frogs-conda-requirements.yaml @@ -6,11 +6,13 @@ dependencies: - frogs =3.2 - emboss =6.6 - flash =1.2 - - cutadapt >=2.8, <=2.10 - - swarm >=2.1, <=3.0.0 - # at least 2.13.4 to fully integrate zlib in vsearch - - vsearch >=2.13.4, <=2.15.1 - - itsx <=1.2 + # need to be >=2.8 + - cutadapt =2.10 + # need to be >=2.1 + - swarm =3.0.0 + # need to be 2.13.4 + - vsearch =2.15.1 + - itsx =1.1.2 - blast =2.10 # - rdptool=2.0.3 # is already included in the frogs dependency - mafft =7.407