6b8b18fac6940d56a6317b23f1aedf107079a277
lrnassar
  Fri Nov 8 17:12:59 2024 -0800
Adding archiving to the mane otto, refs #34761

diff --git src/hg/utils/otto/mane/doMane.py src/hg/utils/otto/mane/doMane.py
index bf346cb..df94218 100644
--- src/hg/utils/otto/mane/doMane.py
+++ src/hg/utils/otto/mane/doMane.py
@@ -8,37 +8,39 @@
         rawBashOutput = subprocess.run(cmd, check=True, shell=True,\
                                        stdout=subprocess.PIPE, universal_newlines=True, stderr=subprocess.STDOUT)
         bashStdoutt = rawBashOutput.stdout
     except subprocess.CalledProcessError as e:
         raise RuntimeError("command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output))
     return(bashStdoutt)
 
 def doMane():
     latestRelease = bash('curl -s https://ftp.ncbi.nlm.nih.gov/refseq/MANE/trackhub/data/ | grep "release_" | tail -1')
     dirName = latestRelease.split(">")[1].split("<")[0]
     version = dirName.split("_")[1].split("/")[0]
     latestReleaseUrl = "https://ftp.ncbi.nlm.nih.gov/refseq/MANE/trackhub/data/"+dirName+"MANE.GRCh38.v"+version+".ensembl.bb"
     workindDir = "/hive/data/outside/otto/mane/mane."+version
     filePathBB = workindDir+"/our.bb"
     filePathBed = workindDir+"/our.bed"
+    filePathArchive = "/usr/local/apache/htdocs-hgdownload/goldenPath/archive/hg38/mane/mane."+version+".bb"
     if not os.path.isfile(filePathBB):
         print("New MANE update: "+latestReleaseUrl)
         bash("mkdir -p "+workindDir)
         bash("bigBedToBed "+latestReleaseUrl+" "+filePathBed)
         bash("bedToBigBed -extraIndex=name "+filePathBed+" /cluster/data/hg38/chrom.sizes "+filePathBB+" -type=bed12+13 -as=$HOME/kent/src/hg/lib/mane.as -tab")
         bash("mkdir -p /gbdb/hg38/mane")
         print("Previous version itemCount:")
         print(bash("bigBedInfo /gbdb/hg38/mane/mane.bb | grep -i itemCount"))
         bash("rm -f /gbdb/hg38/mane/mane.bb")
         bash("ln -s "+filePathBB+" /gbdb/hg38/mane/mane.bb")
+        bash("ln -sf "+filePathBB+" "+filePathArchive)
         print("New version itemCount:")
         print(bash("bigBedInfo /gbdb/hg38/mane/mane.bb | grep -i itemCount"))
         bash("tawk '{print $13, $18, $19, $21, $22, $23, $24}' "+filePathBed+" > "+workindDir+"/our.ixInput")
         bash("ixIxx "+workindDir+"/our.ixInput "+workindDir+"/mane.ix "+workindDir+"/mane.ixx")
         bash("rm -f /gbdb/hg38/mane/mane.ix /gbdb/hg38/mane/mane.ixx")
         bash("ln -s "+workindDir+"/mane.ix /gbdb/hg38/mane")
         bash("ln -s "+workindDir+"/mane.ixx /gbdb/hg38/mane")
         bash("wget https://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/release_"+version+"/README_versions.txt -O "+workindDir+"/README_versions.txt")
         bash("rm -f /gbdb/hg38/mane/README_versions.txt")
         bash("ln -s "+workindDir+"/README_versions.txt /gbdb/hg38/mane")
 
 doMane()