Commit f5037107 authored by mmassaviol's avatar mmassaviol
Browse files

Update r packages installs

(load libraries to detect installation errors)
parent bd4bc9b3
......@@ -141,13 +141,13 @@
],
install: {
dada2: [
"Rscript -e 'library(\"devtools\");devtools::install_github(\"benjjneb/dada2\", ref=\"v1.12\")'",
"Rscript -e 'library(\"devtools\");devtools::install_github(\"benjjneb/dada2\", ref=\"v1.12\");library(\"dada2\")'",
],
phyloseq: [
"Rscript -e 'library(\"devtools\");devtools::install_github(\"joey711/phyloseq\")'"
"Rscript -e 'library(\"devtools\");devtools::install_github(\"joey711/phyloseq\");library(\"phyloseq\")'"
],
biomformat: [
"Rscript -e 'library(\"devtools\");devtools::install_github(\"joey711/biomformat\")'"
"Rscript -e 'library(\"devtools\");devtools::install_github(\"joey711/biomformat\");library(\"biomformat\")'"
],
krona: [
"cd /opt/biotools",
......
......@@ -66,13 +66,14 @@
],
install:
{
DESeq2: ['Rscript -e ''BiocManager::install("DESeq2", version = "3.8",Ncpus=8, clean=TRUE)'''],
apeglm: ['Rscript -e ''BiocManager::install("apeglm", version = "3.8",Ncpus=8, clean=TRUE)'''],
BiocParallel: ['Rscript -e ''BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, clean=TRUE)'''],
tximport: ['Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE)'''],
rhdf5: ['Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE)'''],
GenomicFeatures: ['Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE)'''],
pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE)''']
latticeExtra: ['Rscript -e ''install.packages("latticeExtra",Ncpus=8, clean=TRUE);library("latticeExtra")'''],
DESeq2: ['Rscript -e ''BiocManager::install("DESeq2", version = "3.8",Ncpus=8, clean=TRUE);library("DESeq2")'''],
apeglm: ['Rscript -e ''BiocManager::install("apeglm", version = "3.8",Ncpus=8, clean=TRUE);library("apeglm")'''],
BiocParallel: ['Rscript -e ''BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, clean=TRUE);library("BiocParallel")'''],
tximport: ['Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE);library("tximport")'''],
rhdf5: ['Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE);library("rhdf5")'''],
GenomicFeatures: ['Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE);library("GenomicFeatures")'''],
pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE);library("pheatmap")''']
},
script: deseq2.script.R,
}
......@@ -73,12 +73,12 @@
],
install:
{
limma: ['Rscript -e ''BiocManager::install("limma", version = "3.8",Ncpus=8, clean=TRUE)'''],
edger: ['Rscript -e ''BiocManager::install("edgeR", version = "3.8",Ncpus=8, clean=TRUE)'''],
tximport: ['Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE)'''],
rhdf5: ['Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE)'''],
GenomicFeatures: ['Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE)'''],
pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE)''']
limma: ['Rscript -e ''BiocManager::install("limma", version = "3.8",Ncpus=8, clean=TRUE);library("limma")'''],
edger: ['Rscript -e ''BiocManager::install("edgeR", version = "3.8",Ncpus=8, clean=TRUE);library("edgeR")'''],
tximport: ['Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE);library("tximport")'''],
rhdf5: ['Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE);library("rhdf5")'''],
GenomicFeatures: ['Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE);library("GenomicFeatures")'''],
pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE);library("pheatmap"))''']
},
script: edger.script.R,
}
......@@ -108,7 +108,7 @@
"mv -t ../bin sstacks kmer_filter gstacks tsv2bam process_shortreads populations ustacks clone_filter phasedstacks cstacks process_radtags",
"cd .. && rm -r stacks-2.3b stacks-2.3b.tar.gz"
],
calibrate: ['Rscript -e ''install.packages("calibrate",repos="https://cloud.r-project.org/",Ncpus=8, clean=TRUE)'''],
SNPRelate: ['Rscript -e ''BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean=TRUE)''']
calibrate: ['Rscript -e ''install.packages("calibrate",repos="https://cloud.r-project.org/",Ncpus=8, clean=TRUE);library("calibrate")'''],
SNPRelate: ['Rscript -e ''BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean=TRUE);library("SNPRelate")''']
},
}
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