# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User fubar: ross Lazarus at gmail period com # Date 1283257544 14400 # Node ID 65edd8e2a3a8872252d9008ad2fe9dee7cbd5856 # Parent 7cc9329fd895049827d1bf5436f6aa11bf9d30ed Fix for pdfnup blathering to stdout causing buildbot to barf Small adjustment to file size delta for rgManQQ --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -44,9 +44,9 @@ <param name='grey' value='0' /><output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='30'><extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" - delta = "4000"/> + delta = "10000"/><extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" - delta = "4000" /> + delta = "10000" /><extra_files type="file" name='rgManQQtest1.R' value='rgtestouts/rgManQQ/rgManQQtest1.R' compare="diff" lines_diff="160"/></output></test> --- a/tools/rgenetics/rgManQQ.py +++ b/tools/rgenetics/rgManQQ.py @@ -52,6 +52,7 @@ manhattan = function(chrom=NULL,offset=N lastbase=0 chrlist = unique(d$CHR) nchr = length(chrlist) # may be any number? + if (nchr < 2) { for (x in c(1:nchr)) { i = chrlist[x] # need the chrom number - may not == index if (x == 1) { # first time @@ -62,8 +63,16 @@ manhattan = function(chrom=NULL,offset=N d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP+lastbase } ticks=c(ticks, d[d$CHR==i, ]$pos[floor(length(d[d$CHR==i, ]$pos)/2)+1]) - } - ticklim=c(min(d$pos),max(d$pos)) + ticklim=c(min(d$pos),max(d$pos)) + } + } else { # nchr >= 2 + last = max(offset) + first = min(offset) + ticks = first + t = (last-first)/9 # units per tick + for (x in c(1:9)) ticks = c(ticks,round(x*t)) + ticklim = c(first,last) + } # else if (grey) {mycols=rep(c("gray10","gray60"),max(d$CHR)) } else { mycols=rep(coloursTouse,max(d$CHR)) --- a/tools/rgenetics/rgQC.py +++ b/tools/rgenetics/rgQC.py @@ -270,6 +270,8 @@ def makePlots(markers=[],subjects=[],new rpy.r.dev_off() + fdsto,stofile = tempfile.mkstemp() + sto = open(stofile,'w') import rpy # delay to avoid rpy stdout chatter replacing galaxy file blurb mog = 'mogrify' pdfnup = 'pdfnup' @@ -368,7 +370,7 @@ def makePlots(markers=[],subjects=[],new expl = 'All %s QC Plots joined into a single pdf' % basename vcl = '%s %s --outfile %s ' % (pdfjoin,filestojoin, fullafname) # make single page pdf - x=subprocess.Popen(vcl,shell=True,cwd=newfpath) + x=subprocess.Popen(vcl,shell=True,cwd=newfpath,stderr=sto,stdout=sto) retval = x.wait() row = [expl,afname,fullafname] html.insert(0,row) # last rather than second @@ -377,15 +379,17 @@ def makePlots(markers=[],subjects=[],new expl = 'All %s QC Plots %d by %d to a page' % (basename,nup,nup) vcl = '%s %s --nup %dx%d --frame true --outfile %s' % (pdfnup,afname,nup,nup,fullnfname) # make thumbnail images - x=subprocess.Popen(vcl,shell=True,cwd=newfpath) + x=subprocess.Popen(vcl,shell=True,cwd=newfpath,stderr=sto,stdout=sto) retval = x.wait() row = [expl,nfname,fullnfname] html.insert(1,row) # this goes second vcl = '%s -format jpg -resize %s %s' % (mog, mogresize, os.path.join(newfpath,'*.pdf')) # make thumbnail images - x=subprocess.Popen(vcl,shell=True,cwd=newfpath) + x=subprocess.Popen(vcl,shell=True,cwd=newfpath,stderr=sto,stdout=sto) retval = x.wait() - return html # elements for an ordered list of urls or whatever.. + sto.close() + cruft = open(stofile,'r').readlines() + return html,cruft # elements for an ordered list of urls or whatever.. def RmakePlots(markers=[],subjects=[],newfpath='.',basename='test',nbreaks='100',nup=3,height=8,width=10,rexe=''): @@ -1282,7 +1286,7 @@ if __name__ == "__main__": s = '## starting plotpage, newfpath=%s,m=%s,s=%s/n' % (newfpath,markers[:2],subjects[:2]) alogf.write(s) print s - plotpage = makePlots(markers=markers,subjects=subjects,newfpath=newfpath, + plotpage,cruft = makePlots(markers=markers,subjects=subjects,newfpath=newfpath, basename=basename,nbreaks=nbreaks,height=10,width=8,rgbin=rgbin) #plotpage = RmakePlots(markers=markers,subjects=subjects,newfpath=newfpath,basename=basename,nbreaks=nbreaks,rexe=rexe) @@ -1343,6 +1347,8 @@ if __name__ == "__main__": lf.write('\n'.join(html)) lf.write('<h4>QC run log contents</h4>') lf.write('<pre>%s</pre>' % (''.join(llog))) # plink logs + if len(cruft) > 0: + lf.write('<h2>Blather from pdfnup follows:</h2><pre>%s</pre>' % (''.join(cruft))) # pdfnup lf.write('%s\n<hr>\n' % galhtmlpostfix) lf.close()