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import galaxy-central
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11<div class="document">
12<h4>rgenetics for Galaxy rgHaploView.py, wrapping HaploView</h4><br><div><hr><ul>
13<li><a href="alljoin.pdf">alljoin.pdf - All pdf plots, each on a separate page</a></li>
14<li><a href="allnup.pdf">allnup.pdf - All pdf plots on a single page</a></li>
15<li><a href="1_rgHaploViewtest1.pdf">1_rgHaploViewtest1.pdf - 1_rgHaploViewtest1.pdf</a></li>
16<li><a href="1_rgHaploViewtest1.png">1_rgHaploViewtest1.png - 1_rgHaploViewtest1.png</a></li>
17<li><a href="2_HapMap_YRI_22.pdf">2_HapMap_YRI_22.pdf - Hapmap data</a></li>
18<li><a href="2_HapMap_YRI_22.png">2_HapMap_YRI_22.png - Hapmap data</a></li>
19<li><a href="Chromosome22YRI.LD.PNG">Chromosome22YRI.LD.PNG - Hapmap data</a></li>
20<li><a href="Log_rgHaploViewtest1.txt">Log_rgHaploViewtest1.txt - Log_rgHaploViewtest1.txt</a></li>
21<li><a href="rgHaploViewtest1.info">rgHaploViewtest1.info - rgHaploViewtest1 map data for Haploview input</a></li>
22<li><a href="rgHaploViewtest1.ped">rgHaploViewtest1.ped - rgHaploViewtest1 genotype data for Haploview input</a></li>
23<li><a href="rgHaploViewtest1.ped.LD.PNG">rgHaploViewtest1.ped.LD.PNG - rgHaploViewtest1.ped.LD.PNG</a></li>
24<li><a href="rgHaploViewtest1.ped.TAGS">rgHaploViewtest1.ped.TAGS - rgHaploViewtest1.ped.TAGS Tagger output</a></li>
25<li><a href="rgHaploViewtest1.ped.TESTS">rgHaploViewtest1.ped.TESTS - rgHaploViewtest1.ped.TESTS Tagger output</a></li>
26</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>*****************************************************
27
28Haploview 4.2   Java Version: 1.6.0_03
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30*****************************************************
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36Arguments:      -n      -pairwiseTagging        -pedfile        /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped       -info   /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info      -tagrsqcounts   -tagrsqcutoff   0.8     -ldcolorscheme  RSQ     -maxDistance    200000  -compressedpng  -chromosome     22     
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42Max LD comparison distance = 200000kb
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44Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
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46Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
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48Writing output to rgHaploViewtest1.ped.LD.PNG
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50Starting tagging.
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52Writing output to rgHaploViewtest1.ped.TAGS
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54Writing output to rgHaploViewtest1.ped.TESTS
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56Writing output to rgHaploViewtest1.ped.CHAPS
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58release = 21
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60*****************************************************
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62Haploview 4.2   Java Version: 1.6.0_03
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64*****************************************************
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70Arguments:      -n      -chromosome     22      -panel  YRI     -hapmapDownload -startpos       21784   -endpos 21905   -ldcolorscheme  RSQ     -maxDistance    200000  -compressedpng 
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76Max LD comparison distance = 200000kb
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78Downloading chromosome 22, analysis panel YRI, 21784..21905 from HapMap release 21.
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80Writing output to Chromosome22YRI.LD.PNG
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82This is pdfjoin version 1.20
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84Reading site configuration from /etc/pdfnup.conf
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86  Temporary LaTeX file for this job is /var/tmp/22578.tex
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88  Calling pdflatex...
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90  Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/alljoin.pdf
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92This is pdfnup version 1.20
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94Reading site configuration from /etc/pdfnup.conf
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96Processing alljoin.pdf...
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98  Temporary LaTeX file for this job is /var/tmp/22621-1.tex
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100  Calling pdflatex...
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102  Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/allnup.pdf
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104PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
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106## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region
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110## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0
111
112## executing mogrify -resize 800x400! *.PNG returned 0
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114## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0
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116## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0
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118## executing convert -resize 800x400! Chromosome22YRI.LD.PNG rgHaploViewtest1.tmp.png returned 0
119
120## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'HapMap YRI'" rgHaploViewtest1.tmp.png 2_HapMap_YRI_22.png returned 0
121
122### nimages=2
123
124## executing mogrify -format pdf -resize 800x400! *.png returned 0
125
126## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0
127
128## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0
129</pre><hr></div></body></html>
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