1. MotifDb
  2. inst
  3. scripts
  4. import
  5. importAll.R
Browse code

setwd to original directory at conclusion of loop

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@107894 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 28/08/2015 19:16:27
Showing 1 changed files
inst/scripts/import/importAll.R
History View file @ a0c01d0
... ... 
@@ -6,10 +6,9 @@ library(org.Sc.sgd.db)
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 # biocLite(c("org.Ce.eg.db", "org.Dm.eg.db", "org.Hs.eg.db", "org.Mm.eg.db", "org.Sc.sgd.db"))
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 directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab",
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-                 "uniprobe", "jaspar2014",
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+                 "uniprobe", "jaspar2014", "jolma2013", "cisbp")
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                  #"HOCOMOCO",
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-                 "cisbp")
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-#directories <- directories[2]
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+
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 starting.directory <- getwd()
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 stopifnot(basename(starting.directory) == "import")
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... ... 
@@ -26,3 +25,4 @@ for(directory in directories){
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     run(repoRoot)
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     }
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+setwd(starting.directory)
Browse code

added explicit loads of org packages (eg, library(org.Hs.eg.db)) after collecting them all from the per-source import.R files. with these loaded at the start (and also see commented-out biocLite load.packages command) all of the dependicies of the various import scripts can be installed as you start

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@107890 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 28/08/2015 18:58:16
Showing 1 changed files
inst/scripts/import/importAll.R
History View file @ 58c0eb8
... ... 
@@ -1,3 +1,10 @@
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+library(org.Ce.eg.db)
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+library(org.Dm.eg.db)
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+library(org.Hs.eg.db)
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+library(org.Mm.eg.db)
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+library(org.Sc.sgd.db)
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+# biocLite(c("org.Ce.eg.db", "org.Dm.eg.db", "org.Hs.eg.db", "org.Mm.eg.db", "org.Sc.sgd.db"))
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+
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 directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab",
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                  "uniprobe", "jaspar2014",
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                  #"HOCOMOCO",
... ... 
@@ -6,8 +13,9 @@ directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab",
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 starting.directory <- getwd()
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 stopifnot(basename(starting.directory) == "import")
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-repoRoot <- "~/s/data/public/TFBS"
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+#repoRoot <- "~/s/data/public/TFBS"
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 #repoRoot <- "/shared/silo_researcher/Morgan_M/BioC/MotifDb"
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+repoRoot <- "/fh/fast/morgan_m/BioC/MotifDb-raw-data"
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 for(directory in directories){
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     print(noquote(sprintf("--- importing %s", directory)))
Browse code

cisbp now successfully added: unit tets pass, man page for package updated

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@107858 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 28/08/2015 04:39:12
Showing 1 changed files
inst/scripts/import/importAll.R
History View file @ a51f6d0
... ... 
@@ -1,15 +1,19 @@
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-directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab", "uniprobe")
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+directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab",
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+                 "uniprobe", "jaspar2014",
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+                 #"HOCOMOCO",
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+                 "cisbp")
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+#directories <- directories[2]
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 starting.directory <- getwd()
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 stopifnot(basename(starting.directory) == "import")
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-#repoRoot <- "~/s/data/public/TFBS"
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-repoRoot <- "/shared/silo_researcher/Morgan_M/BioC/MotifDb"
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+repoRoot <- "~/s/data/public/TFBS"
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+#repoRoot <- "/shared/silo_researcher/Morgan_M/BioC/MotifDb"
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 for(directory in directories){
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     print(noquote(sprintf("--- importing %s", directory)))
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     setwd(file.path(starting.directory, directory))
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-    source("test.R")
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-    run.tests(repoRoot)
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+    #source("test.R")
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+    #run.tests(repoRoot)
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     source("import.R")
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     run(repoRoot)
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     }
Browse code

added and tested uniprobe to the 'importAll' operation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@75475 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 09/04/2013 20:49:43
Showing 1 changed files
inst/scripts/import/importAll.R
History View file @ a2447d6
... ... 
@@ -1,8 +1,8 @@
1 
-directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab")#   "uniprobe"
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+directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab", "uniprobe")
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 starting.directory <- getwd()
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 stopifnot(basename(starting.directory) == "import")
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-repoRoot <- "~/s/data/public/TFBS"
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+#repoRoot <- "~/s/data/public/TFBS"
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 repoRoot <- "/shared/silo_researcher/Morgan_M/BioC/MotifDb"
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 for(directory in directories){
Browse code

added repoRoot assignment, only mention in all files

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@75384 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 05/04/2013 20:39:49
Showing 1 changed files
inst/scripts/import/importAll.R
History View file @ b52fba5
... ... 
@@ -2,15 +2,15 @@ directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab")#   "u
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 starting.directory <- getwd()
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 stopifnot(basename(starting.directory) == "import")
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-kDataDir <- "~/s/data/public/TFBS"
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-kDataDir <- "/shared/silo_researcher/Morgan_M/BioC/MotifDb"
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+repoRoot <- "~/s/data/public/TFBS"
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+repoRoot <- "/shared/silo_researcher/Morgan_M/BioC/MotifDb"
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 for(directory in directories){
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     print(noquote(sprintf("--- importing %s", directory)))
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     setwd(file.path(starting.directory, directory))
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     source("test.R")
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-    run.tests(kDataDir)
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+    run.tests(repoRoot)
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     source("import.R")
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-    run(kDataDir)
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+    run(repoRoot)
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     }
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Browse code

locally appropriate repo root dir, 'kDataDir', passed to run.tests and run

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@75370 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 05/04/2013 17:44:42
Showing 1 changed files
inst/scripts/import/importAll.R
History View file @ aec22c5
... ... 
@@ -2,12 +2,15 @@ directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab")#   "u
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 starting.directory <- getwd()
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 stopifnot(basename(starting.directory) == "import")
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+kDataDir <- "~/s/data/public/TFBS"
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+kDataDir <- "/shared/silo_researcher/Morgan_M/BioC/MotifDb"
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+
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 for(directory in directories){
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     print(noquote(sprintf("--- importing %s", directory)))
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     setwd(file.path(starting.directory, directory))
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-    #source("test.R")
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-    #run.tests()
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+    source("test.R")
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+    run.tests(kDataDir)
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     source("import.R")
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-    run()
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+    run(kDataDir)
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     }
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Browse code

disabled automatic testing

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@75356 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 05/04/2013 16:50:33
Showing 1 changed files
inst/scripts/import/importAll.R
History View file @ abcbfdb
... ... 
@@ -5,8 +5,8 @@ stopifnot(basename(starting.directory) == "import")
5 5 
 for(directory in directories){
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     print(noquote(sprintf("--- importing %s", directory)))
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     setwd(file.path(starting.directory, directory))
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-    source("test.R")
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-    run.tests()
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+    #source("test.R")
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+    #run.tests()
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     source("import.R")
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     run()
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     }
Browse code

first version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@75353 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 05/04/2013 16:36:14
Showing 1 changed files
inst/scripts/import/importAll.R
History View file @ c8ccca2
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,13 @@
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+directories <- c("flyFactorSurvey", "hPDI", "jaspar", "ScerTF", "stamlab")#   "uniprobe"
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+starting.directory <- getwd()
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+stopifnot(basename(starting.directory) == "import")
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+
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+for(directory in directories){
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+    print(noquote(sprintf("--- importing %s", directory)))
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+    setwd(file.path(starting.directory, directory))
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+    source("test.R")
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+    run.tests()
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+    source("import.R")
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+    run()
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+    }
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+