From 01429c172b98e43327bb34e93d2a6fb77cfc7db4 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Fri, 9 Aug 2024 10:45:23 -0400 Subject: [PATCH 1/3] Document MEME suite installation --- Doc/Prepare-Ubuntu-22.04-HOWTO.md | 29 +++++++++++++++++++++++++++++ Doc/Prepare-macOS-Big-Sur-HOWTO.md | 29 +++++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) diff --git a/Doc/Prepare-Ubuntu-22.04-HOWTO.md b/Doc/Prepare-Ubuntu-22.04-HOWTO.md index 26aee630..891db2fb 100644 --- a/Doc/Prepare-Ubuntu-22.04-HOWTO.md +++ b/Doc/Prepare-Ubuntu-22.04-HOWTO.md @@ -1399,6 +1399,35 @@ 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 + ./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=$PATH:/opt/meme/libexec/meme-5.5.5 + export MEME_BIN=/opt/meme/bin + +#### Testing + +From the `biocbuild` account, log back in then try to build and check the +**MotifPeeker** package: + + cd ~/bbs-3.19-bioc/meat/ + ../R/bin/R CMD build MotifPeeker + ## 4. Set up other builds diff --git a/Doc/Prepare-macOS-Big-Sur-HOWTO.md b/Doc/Prepare-macOS-Big-Sur-HOWTO.md index 02f6c799..5410026a 100644 --- a/Doc/Prepare-macOS-Big-Sur-HOWTO.md +++ b/Doc/Prepare-macOS-Big-Sur-HOWTO.md @@ -1578,6 +1578,35 @@ You might need to logout and login again before trying this: R CMD check --no-vignettes rmspc_X.Y.Z.tar.gz +### 4.11 Install MEME suite + +Required by Bioconductor package **MotifPeeker**. + +Download, configure and install MEME suite. Set `MEME_VERSION` to the latest +version. + + MEME_VERSION=5.5.5 + MEME_PATH=/opt + curl -L -O https://meme-suite.org/meme/meme-software/$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 From 5542d9783a15e8fa13fe6b5381ab17ca57a868fc Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Fri, 27 Sep 2024 13:07:23 -0400 Subject: [PATCH 2/3] Add Perl modules for MEME suite --- Doc/Prepare-Ubuntu-22.04-HOWTO.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/Doc/Prepare-Ubuntu-22.04-HOWTO.md b/Doc/Prepare-Ubuntu-22.04-HOWTO.md index 891db2fb..9f600386 100644 --- a/Doc/Prepare-Ubuntu-22.04-HOWTO.md +++ b/Doc/Prepare-Ubuntu-22.04-HOWTO.md @@ -1411,6 +1411,17 @@ version. 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 missing + 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 From ba26bf7732f4ce8d58b88a18ad7e3a0d87010975 Mon Sep 17 00:00:00 2001 From: jwokaty Date: Wed, 9 Oct 2024 12:06:19 -0400 Subject: [PATCH 3/3] Update Prepare-Ubuntu-22.04-HOWTO.md Remove 'missing' --- Doc/Prepare-Ubuntu-22.04-HOWTO.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Doc/Prepare-Ubuntu-22.04-HOWTO.md b/Doc/Prepare-Ubuntu-22.04-HOWTO.md index 9f600386..ba7a9289 100644 --- a/Doc/Prepare-Ubuntu-22.04-HOWTO.md +++ b/Doc/Prepare-Ubuntu-22.04-HOWTO.md @@ -1417,7 +1417,7 @@ 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 missing + sudo cpanm -vn XML::Simple sudo cpanm -vn Sys::Info Configure