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comparison mutspecNmf_wrapper.sh @ 5:097ae310ced0 draft

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Uploaded
author iarc
date Fri, 29 Apr 2016 05:14:23 -0400
parents 916846f73e25
children 46a10309dfe2
comparison
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4:916846f73e25 5:097ae310ced0
1 #!/bin/bash 1 #!/bin/bash
2 2
3 ######################################### 3 #########################################
4 ### SPECIFY THE NUMBER OF CPU ### 4 ### SPECIFY THE NUMBER OF CPU ###
5 ######################################### 5 #########################################
6 cpu=8 6 cpu=1
7 7
8 8
9 9
10 10
11 html=$1;shift 11 html=$1;shift
12 parameters=$1;shift 12 parameters=$1;shift
13 source=$1;shift 13 source=$1;shift
14 input=$1 14 input=$1
15 15
16 if [[ $source == "html" ]] 16 if [[ $source == "html" ]]
17 then input=${input%%.*}_files/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt 17 then input=${input%%.*}_files/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt
18 fi 18 fi
19 19
20 output_dir=${html%%.*}_files 20 output_dir=${html%%.*}_files
21 mkdir $output_dir 21 mkdir $output_dir
42 if [[ ! -e "$output_dir/NMF/Figures/Heatmap_MixtureCoeff.png" ]]; then 42 if [[ ! -e "$output_dir/NMF/Figures/Heatmap_MixtureCoeff.png" ]]; then
43 echo "WARNING: NMF package can't plot the heatmap when the samples size is above 300. <br/>" >> $html 43 echo "WARNING: NMF package can't plot the heatmap when the samples size is above 300. <br/>" >> $html
44 else 44 else
45 echo "<td> <center> <a href="NMF/Figures/Heatmap_MixtureCoeff.png">" >> $html 45 echo "<td> <center> <a href="NMF/Figures/Heatmap_MixtureCoeff.png">" >> $html
46 echo "<img src="NMF/Figures/Heatmap_MixtureCoeff.png" /></a> <center> </td>" >> $html 46 echo "<img src="NMF/Figures/Heatmap_MixtureCoeff.png" /></a> <center> </td>" >> $html
47 fi 47 fi
48 echo "</tr>" >> $html 48 echo "</tr>" >> $html
49 echo "</table>" >> $html 49 echo "</table>" >> $html
50 50
51 echo "<br/><br/>" >> $html 51 echo "<br/><br/>" >> $html
52 52