From 0509ffaff5677d8635421e35fe52b933be27ac6d Mon Sep 17 00:00:00 2001 From: andrewjpage Date: Fri, 12 Jun 2015 09:37:43 +0100 Subject: [PATCH 1/3] mafft speedups up prank --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 987f3ca..d41bf2f 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ Roary takes annotated assemblies as input in GFF3 format, such as those produced Assuming you have root on your system, all the dependancies can be installed using apt and cpanm (only tested on Ubuntu 14.04). ``` -sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank +sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft sudo cpanm -f Bio::Roary ``` @@ -38,7 +38,7 @@ Assuming you have [homebrew](http://brew.sh/) (OSX) or [linuxbrew](http://brew.s ``` brew tap homebrew/science -brew install bedtools cd-hit blast mcl parallel prank +brew install bedtools cd-hit blast mcl parallel prank mafft cpanm -f Bio::Roary ``` From dbaf76388902ca67216d87f810a977a5128a23e9 Mon Sep 17 00:00:00 2001 From: andrewjpage Date: Fri, 12 Jun 2015 09:41:56 +0100 Subject: [PATCH 2/3] add exonerate to speedup prank --- README.md | 4 ++-- install_dependencies.sh | 4 +++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index d41bf2f..fc1ca16 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ Roary takes annotated assemblies as input in GFF3 format, such as those produced Assuming you have root on your system, all the dependancies can be installed using apt and cpanm (only tested on Ubuntu 14.04). ``` -sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft +sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft exonerate sudo cpanm -f Bio::Roary ``` @@ -38,7 +38,7 @@ Assuming you have [homebrew](http://brew.sh/) (OSX) or [linuxbrew](http://brew.s ``` brew tap homebrew/science -brew install bedtools cd-hit blast mcl parallel prank mafft +brew install bedtools cd-hit blast mcl parallel prank mafft exonerate cpanm -f Bio::Roary ``` diff --git a/install_dependencies.sh b/install_dependencies.sh index fb461dc..475db86 100755 --- a/install_dependencies.sh +++ b/install_dependencies.sh @@ -37,7 +37,9 @@ sudo apt-get install -y -q g++ \ libdb-dev \ libssl-dev \ ncbi-blast+ \ - mcl + mcl \ + exonerate \ + mafft download () { download_url=$1 From 5bfae6ac59d0e0baaa5ca51ba56ec62a4ea3059b Mon Sep 17 00:00:00 2001 From: andrewjpage Date: Fri, 12 Jun 2015 09:47:03 +0100 Subject: [PATCH 3/3] indenting --- install_dependencies.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/install_dependencies.sh b/install_dependencies.sh index 475db86..992f27a 100755 --- a/install_dependencies.sh +++ b/install_dependencies.sh @@ -38,8 +38,8 @@ sudo apt-get install -y -q g++ \ libssl-dev \ ncbi-blast+ \ mcl \ - exonerate \ - mafft + exonerate \ + mafft download () { download_url=$1