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Update docs
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lmrodriguezr committed Feb 8, 2024
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37 changes: 21 additions & 16 deletions manual/part2/requirements/apt-get.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
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4 changes: 2 additions & 2 deletions manual/part2/requirements/mytaxa.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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 ../.. )
```
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