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added bioconductor liraries for RNA-seq in makefile
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rioualen committed Jun 2, 2016
1 parent 7b03b82 commit e4185c4
Showing 1 changed file with 8 additions and 7 deletions.
15 changes: 8 additions & 7 deletions scripts/makefiles/install_tools_and_libs.mk
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ usage:
UBUNTU_VER_NAME="trusty"
CRAN_MIRROR="http://cran.univ-lyon1.fr"
CRAN_PACK_LIST='XML', 'bPeaks', 'caTools'
BIOC_PACK_LIST='affy', 'biomaRt', 'Rsamtools'
BIOC_PACK_LIST='affy', 'biomaRt', 'Rsamtools', 'edgeR', 'DESqe2', 'GenomicFeatures'
PUB_KEY=51716619E084DAB9 F7B8CEA6056E8E56

BEDTOOLS_VER=2.24.0
Expand Down Expand Up @@ -105,7 +105,7 @@ create_bin:

## Initialize a bashrc file, which will allow any user to load the
## path and configuration at once.
update__bashrc: create_bin
update_bashrc:
@echo 'alias ls="ls --color"' >> $(BASHRC)
@echo 'alias rm="rm -i"' >> $(BASHRC)
@echo "" >> $(BASHRC)
Expand Down Expand Up @@ -216,12 +216,12 @@ sratoolkit:
# Quality assessment & trimming
# ----------------------------------------------------------------

fastqc: create_bin
fastqc:
cd $(SOURCE_DIR); \
wget --no-clobber http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v$(FASTQC_VER).zip;\
unzip -o fastqc_v$(FASTQC_VER).zip; \
chmod +x FastQC/fastqc; \
ln -s -f $(SOURCE_DIR)/FastQC/fastqc $(BIN_DIR)/
ln -s -f $(SOURCE_DIR)/FastQC/fastqc $(BIN_DIR)/fastqc

sickle:
cd $(SOURCE_DIR); \
Expand All @@ -230,6 +230,7 @@ sickle:
make; \
cp sickle $(BIN_DIR)


# ----------------------------------------------------------------
# Mapping tools
# ----------------------------------------------------------------
Expand Down Expand Up @@ -280,12 +281,12 @@ macs1:


macs2:
sudo pip install MACS2;
sudo pip install MACS2

spp:
cd $(SOURCE_DIR);\
wget -nc http://compbio.med.harvard.edu/Supplements/ChIP-seq/spp_$(SPP_VER).tar.gz;\
sudo R CMD INSTALL spp_$(SPP_VER).tar.gz; \
sudo R CMD INSTALL spp_$(SPP_VER).tar.gz

## Currently not working -> see w/ S.Wilder, new version to come?
#swembl:
Expand Down Expand Up @@ -347,7 +348,7 @@ desktop_and_x2go:
sudo apt-get install -y --no-install-recommends ubuntu-mate-core ubuntu-mate-desktop
sudo apt-get install -y mate-desktop-environment-extra
sudo apt-get install -y mate-notification-daemon caja-gksu caja-open-terminal
sudo apt-get install -y ambiance-colors radiance-colors;
sudo apt-get install -y ambiance-colors radiance-colors



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