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Document MEME suite installation #422

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01429c1
Document MEME suite installation
jwokaty Aug 9, 2024
5542d97
Add Perl modules for MEME suite
jwokaty Sep 27, 2024
ba26bf7
Update Prepare-Ubuntu-22.04-HOWTO.md
jwokaty Oct 9, 2024
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40 changes: 40 additions & 0 deletions Doc/Prepare-Ubuntu-22.04-HOWTO.md
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Original file line number Diff line number Diff line change
Expand Up @@ -1399,6 +1399,46 @@ From the `biocbuild` account, try to build and check the **rmspc** package:
../R/bin/R CMD check --no-vignettes rmspc_X.Y.Z.tar.gz


### 3.8 Install MEME suite

Required by Bioconductor package **MotifPeeker**.

Download, configure and install MEME suite. Set `MEME_VERSION` to the latest
version.

MEME_VERSION=5.5.5
MEME_PATH=/opt
curl -L -O https://meme-suite.org/meme/meme-software/$MEME_VERSION/meme-$MEME_VERSION.tar.gz
tar zxf meme-$MEME_VERSION.tar.gz
cd meme-$MEME_VERSION

Install Perl dependences, which can be descovered by `perl scripts/dependencies.pl'. Install
with `cpan` or `cpanm`:

sudo apt search libexpat-dev | grep installed # Install if needed for XML::Simple
sudo cpanm -vn HTML::Template
sudo cpanm -vn XML::Simple
sudo cpanm -vn Sys::Info

Configure

./configure --prefix=$MEME_PATH/meme --with-url=http://meme-suite.org/ --enable-build-libxml2 --enable-build-libxslt
sudo make install

Add MEME suite to the path and export `MEME_BIN` in `/etc/profile`:

export PATH=$PATH:/opt/meme/bin
export PATH=$PATH:/opt/meme/libexec/meme-5.5.5
export MEME_BIN=/opt/meme/bin

#### Testing

From the `biocbuild` account, log back in then try to build and check the
**MotifPeeker** package:

cd ~/bbs-3.19-bioc/meat/
../R/bin/R CMD build MotifPeeker


## 4. Set up other builds

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29 changes: 29 additions & 0 deletions Doc/Prepare-macOS-Big-Sur-HOWTO.md
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Expand Up @@ -1578,6 +1578,35 @@ You might need to logout and login again before trying this:
R CMD check --no-vignettes rmspc_X.Y.Z.tar.gz


### 4.11 Install MEME suite

Required by Bioconductor package **MotifPeeker**.

Download, configure and install MEME suite. Set `MEME_VERSION` to the latest
version.

MEME_VERSION=5.5.5
MEME_PATH=/opt
curl -L -O https://meme-suite.org/meme/meme-software/$MEME_VERSION/meme-$MEME_VERSION.tar.gz
tar zxf meme-$MEME_VERSION.tar.gz
cd meme-$MEME_VERSION
./configure --prefix=$MEME_PATH/meme --with-url=http://meme-suite.org/ --enable-build-libxml2 --enable-build-libxslt
sudo make install

Add MEME suite to the path and export `MEME_BIN` in `/etc/profile`:

export PATH=$PATH:/opt/meme/bin
export PATH=$PATH:/opt/meme/libexec/meme-5.5.5
export MEME_BIN=/opt/meme/bin

#### Testing

From the `biocbuild` account, log back in then try to build and check the
**MotifPeeker** package:

cd ~/bbs-3.19-bioc/meat/
../R/bin/R CMD build MotifPeeker


## 5. Set up other builds

Expand Down