programs

# Visualisation
tablet
#artemis
#aliview

# QC
trimmomatic
kraken
fastqc

#Mapping
bwa
minimap2
bowtie2
bowtie
samtools

# Variant calling
bcftools
delly
gatk4


# Assembly
velvet
perl-velvetoptimiser

# Transcriptomics
htseq

# GWAS
#gPLINK2.jar
plink
#emmax

# Microbiome
mothur
krona

# Phylogenetics
beast
beagle-lib
#tempest
#figtree
tracer
mafft
raxml

#minION
#albacore

# Misc 
#R

# R
install.packages(c("gplots","dplyr","data.table","futile.logger","ggplot2","optparse","plyr","readr","reshape2","scales","viridis","yaml"))
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")






import sys

sys.stdout.write("conda install")
x = ""
for l in open("programs.txt"):
	if l[0]=="#": continue
	if l=="": continue
	if "install.packages" in l: x = l; continue
	sys.stdout.write(" "+l.rstrip())
sys.stdout.write("\n")

print(x)