diff --git a/manual/part2/requirements/apt-get.md b/manual/part2/requirements/apt-get.md index dd8d8a5..0e377b9 100644 --- a/manual/part2/requirements/apt-get.md +++ b/manual/part2/requirements/apt-get.md @@ -13,10 +13,10 @@ Run: ```bash sudo apt-get update sudo apt-get install \ - ruby ruby-sqlite3 r-base sqlite3 python \ + ruby ruby-sqlite3 r-base sqlite3 \ libcurl4-openssl-dev zlib1g zlib1g-dev \ - ncbi-blast+ hmmer bedtools idba prodigal \ - mcl barrnap diamond-aligner trnascan-se + ncbi-blast+ hmmer bedtools idba prodigal mcl barrnap \ + diamond-aligner trnascan-se fastp fastani seqtk ``` ## Additional Software @@ -26,29 +26,34 @@ you can install it in your 64bit Linux machine using: ```bash ## FaQCs -curl -Lso FaQCs \ +wget -O FaQCs \ "https://github.com/LANL-Bioinformatics/FaQCs/releases/download/2.10/FaQCs_linux_x86_64" sudo install FaQCs /usr/bin/ && rm FaQCs ## Falco -curl -Lso falco.tar.gz \ - "https://github.com/smithlabcode/falco/releases/download/v0.2.4/falco-0.2.4.tar.gz" +wget -O falco.tar.gz \ + "https://github.com/smithlabcode/falco/releases/download/v1.2.1/falco-1.2.1.tar.gz" tar zxf falco.tar.gz -( cd falco-0.2.4 \ +( cd falco-1.2.1 \ && ./configure CXXFLAGS="-O3 -Wall" \ && make && sudo make install ) > /dev/null -rm -rf falco-0.2.4 +rm -rf falco-1.2.1 falco.tar.gz +``` + +# JAVA VM -## Fastp -curl -Lso fastp "http://opengene.org/fastp/fastp" -sudo install fastp /usr/bin/ && rm fastp +If you want support for RDP classifications, you'll need any working Java VM. +For example, you could install Temurin as follows: -# FastANI -curl -Lso fastani-Linux64-v1.33.zip \ - "https://github.com/ParBLiSS/FastANI/releases/download/v1.33/fastani-Linux64-v1.33.zip" -unzip fastani-Linux64-v1.33.zip fastANI > /dev/null && rm fastani-Linux64-v1.33.zip -sudo install fastANI /usr/bin/ && rm fastANI +```bash +wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public \ + | sudo apt-key add - +echo "deb https://packages.adoptium.net/artifactory/deb \ + $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" \ + | sudo tee /etc/apt/sources.list.d/adoptium.list +sudo apt-get update +sudo apt-get install temurin-21-jdk ``` ## MyTaxa utils diff --git a/manual/part2/requirements/mytaxa.md b/manual/part2/requirements/mytaxa.md index e3e2839..3a5f2ae 100644 --- a/manual/part2/requirements/mytaxa.md +++ b/manual/part2/requirements/mytaxa.md @@ -18,7 +18,7 @@ echo 'export PATH=$HOME/apps/bin:$PATH' >> ~/.miga_modules ## MyTaxa ```bash -curl -L \ +wget -O - \ https://github.com/luo-chengwei/MyTaxa/archive/master.tar.gz | tar zx cd MyTaxa-master make @@ -33,7 +33,7 @@ If you followed the instructions for [conda](conda.md) or [Homebrew](brew.md), you already have Krona. If you still need to install Krona, simply execute: ```bash -curl -L \ +wget -O - \ https://github.com/marbl/Krona/archive/master.tar.gz | tar zx ( cd Krona-master/KronaTools && ./install.pl --prefix ../.. ) ```