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Update Ghana Installation software authored by ndomassi.tando_ird.fr's avatar ndomassi.tando_ird.fr
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Ghana-Installation-software.md
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...@@ -13,7 +13,7 @@ URL : http://sanger-pathogens.github.io/Artemis/Artemis/ ...@@ -13,7 +13,7 @@ URL : http://sanger-pathogens.github.io/Artemis/Artemis/
Add /usr/local/bioinfo/artemis to the path : Add /usr/local/bioinfo/artemis to the path :
echo 'export PATH=$PATH:/usr/local/artemis/' >>/etc/profile echo 'export PATH=$PATH:/usr/local/bioinfo/artemis/' >>/etc/profile
source /etc/profile source /etc/profile
### Usage : ### Usage :
...@@ -50,14 +50,14 @@ Modify the following file: ...@@ -50,14 +50,14 @@ Modify the following file:
with: with:
INCLUDES = /usr/local/PATH_TO_BAMTOOLS/include INCLUDES = /usr/local/bioinfo/PATH_TO_BAMTOOLS/include
LIBS = /usr/local/PATH_TO_BAMTOOLS/lib/libbamtools.a -lz LIBS = /usr/local/bioinfo/PATH_TO_BAMTOOLS/lib/libbamtools.a -lz
Example: Example:
INCLUDES = /usr/local/bioinfo/bamtools-2.3/include INCLUDES = /usr/local/bioinfo/bamtools-2.3/include
LIBS = /usr/local/bamtools-2.3/lib/libbamtools.a -lz LIBS = /usr/local/bioinfo/bamtools-2.3/lib/libbamtools.a -lz
Modify the following file: Modify the following file:
...@@ -66,14 +66,14 @@ Modify the following file: ...@@ -66,14 +66,14 @@ Modify the following file:
with: with:
BAMTOOLS = /usr/local/PATH_TO_BAMTOOLS/include BAMTOOLS = /usr/local/bioinfo/PATH_TO_BAMTOOLS/include
LIBS = /usr/local/PATH_TO_BAMTOOLS/lib/libbamtools.a -lz LIBS = /usr/local/bioinfo/PATH_TO_BAMTOOLS/lib/libbamtools.a -lz
Example: Example:
BAMTOOLS = /usr/local/bioinfo/bamtools-2.3/include BAMTOOLS = /usr/local/bioinfo/bamtools-2.3/include
LIBS = /usr/local/bamtools-2.3/lib/libbamtools.a -lz LIBS = /usr/local/bioinfo/bamtools-2.3/lib/libbamtools.a -lz
The launch the compilation: The launch the compilation:
...@@ -116,7 +116,7 @@ bam-readcount does not support in source builds. Create a new build directory, e ...@@ -116,7 +116,7 @@ bam-readcount does not support in source builds. Create a new build directory, e
cmake .. cmake ..
make make
cd .. cd ..
cp -r bam-readcount /usr/local cp -r bam-readcount /usr/local/bioinfo
Add /usr/local/bioinfo/bam-readcount/build/bin to the path : Add /usr/local/bioinfo/bam-readcount/build/bin to the path :
...@@ -317,7 +317,12 @@ URL: http://exon.gatech.edu/GeneMark/ ...@@ -317,7 +317,12 @@ URL: http://exon.gatech.edu/GeneMark/
mv gm_et_linux_64 GeneMark-ES-4.38 mv gm_et_linux_64 GeneMark-ES-4.38
cp -r GeneMark-ES-4.38 /usr/local/bioinfo cp -r GeneMark-ES-4.38 /usr/local/bioinfo
The default perl used in the perl scripts of GenMark-ES is `/usr/bin/perl`you may have to change it with your own path to perl.
For example if `/usr/local/perl-5.24.0/bin/perl` is your default perl, go into /usr/local/bioinfo/GeneMark-ES-4.38/gmes_peta and type the following command:
find . -type f -exec sed -i -e 's/\/usr\/bin\/perl/\/usr\/local\/perl-5.24.0\/bin\/perl/g' {} \;
Add /usr/local/bioinfo/GeneMark-ES-4.38 to the path : Add /usr/local/bioinfo/GeneMark-ES-4.38 to the path :
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