@@ -11,20 +11,19 @@

 # through svn).

 ##########################################################

-fixMakefile = function() {

+enableMaintainerMode = function() {

     mkfile = file.path("src/Makefile")

     txt = readLines(mkfile)

     txt2 = gsub("(--disable-maintainer-mode.*)", "\\\\ # \\1;", txt)

     writeLines(txt2, con = mkfile)

 }

-unfixMakefile = function() {

+disableMaintainerMode = function() {

     mkfile = file.path("src/Makefile")

     txt = readLines(mkfile)

     txt2 = gsub("\\\\ # (.*);", "\\1", txt)

     writeLines(txt2, con = mkfile)

 }

-    

 updateGMAPSrc <- function() {

@@ -60,13 +59,14 @@ updateGSTRUCTSrc <- function() {

   if (file.exists(extractDir)) {

     unlink(extractDir, recursive=TRUE)

   }

-  dir.create(extractDir)

+  dir.create(extractDir, recursive=TRUE)

   svnCheckoutDir <- .getSVNProj(projectSVNURL, extractDir)

   on.exit(unlink(svnCheckoutDir, recursive=TRUE), add=TRUE)

   setwd(svnCheckoutDir)

-  .bootstrapSVNCheckout(bootstrap.script)  

-  .configureSrc(program)

+  .bootstrapSVNCheckout(bootstrap.script)

+  samtoolsPath <- file.path(startingDir, "src", "samtools")

+  .configureSrc(program, samtoolsPath)

   .makeDist()

   .extractDistTarballIntoSrcDirectory(extractDir)

   invisible(TRUE)

@@ -107,12 +107,17 @@ updateGSTRUCTSrc <- function() {

   }

 }

-.configureSrc <- function(program) {

+.configureSrc <- function(program, samtoolsPath = NULL) {

   ##--with-gmapdb=${GMAPDB} --prefix=${PREFIX}

   ##configure. Set

   ##run a "make dist" to build a tarball

   command <- "./configure --disable-fulldist"

-  ##if (program == "gstruct") command <- paste(command, "--disable-binaries")

+  if (!is.null(samtoolsPath)) {

+      command <- paste0(command, " --with-samtools-lib=", samtoolsPath)

+  }

+  if (program == "gstruct") {

+      command <- paste(command, "--disable-binaries")

+  }

   if (!system(command) == 0) {

     stop("unable to configure")

   }

@@ -127,10 +132,7 @@ updateGSTRUCTSrc <- function() {

 }

 .makeDist <- function() {

-  ##run a "make dist" to build a tarball

-  if (!system("make distcheck") == 0) {

-    stop("unable to 'make dist'")

-  }  

+    system("make && make dist") ## possibly more robust than direct "make dist"

 }

 .extractDistTarballIntoSrcDirectory <- function(extractDir) {

@@ -38,7 +38,7 @@ updateGMAPSrc <- function() {

 }

 updateGSTRUCTSrc <- function() {

   #gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/releases/internal-2014-04-09"

-    gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/branches/2014-07-10-amino-acid-tally"

+    gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

   extractDirGstruct <- file.path(getwd(), "src/gstruct")

   .bootstrapAndExtract(projectSVNURL=gstructSVNProj,

                        extractDir=extractDirGstruct,

@@ -38,7 +38,7 @@ updateGMAPSrc <- function() {

 }

 updateGSTRUCTSrc <- function() {

   #gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/releases/internal-2014-04-09"

-    gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

+    gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/branches/2014-07-10-amino-acid-tally"

   extractDirGstruct <- file.path(getwd(), "src/gstruct")

   .bootstrapAndExtract(projectSVNURL=gstructSVNProj,

                        extractDir=extractDirGstruct,

@@ -38,7 +38,7 @@ updateGMAPSrc <- function() {

 }

 updateGSTRUCTSrc <- function() {

   #gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/releases/internal-2014-04-09"

-    gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/branches/2014-07-10-amino-acid-tally"

+    gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

   extractDirGstruct <- file.path(getwd(), "src/gstruct")

   .bootstrapAndExtract(projectSVNURL=gstructSVNProj,

                        extractDir=extractDirGstruct,

@@ -8,12 +8,28 @@

 # "--disable-maintainer-mode" argument passed in src/Makefile to the

 # respective configure scripts. This was added to avoid regenerating

 # autotools artifacts on user machines (the timestamp protection fails

-# through svn). ALSO make sure not to remove the maintainer mode macro call

-# in gstruct|gmap/configure.ac (revert the change from the update).

+# through svn).

 ##########################################################

+fixMakefile = function() {

+    mkfile = file.path("src/Makefile")

+    txt = readLines(mkfile)

+    txt2 = gsub("(--disable-maintainer-mode.*)", "\\\\ # \\1;", txt)

+    writeLines(txt2, con = mkfile)

+}

+

+unfixMakefile = function() {

+    mkfile = file.path("src/Makefile")

+    txt = readLines(mkfile)

+    txt2 = gsub("\\\\ # (.*);", "\\1", txt)

+    writeLines(txt2, con = mkfile)

+}

+    

+

 updateGMAPSrc <- function() {

-  gmapSVNProj <-

+

+    mkfile = 

+    gmapSVNProj <-

     "http://resscm/bioinfo/projects/gmap/releases/internal-2013-10-01"

   extractDirGmap <- file.path(getwd(), "src/gmap")

   .bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

@@ -21,7 +37,8 @@ updateGMAPSrc <- function() {

 }

 updateGSTRUCTSrc <- function() {

-  gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

+  #gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/releases/internal-2014-04-09"

+    gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/branches/2014-07-10-amino-acid-tally"

   extractDirGstruct <- file.path(getwd(), "src/gstruct")

   .bootstrapAndExtract(projectSVNURL=gstructSVNProj,

                        extractDir=extractDirGstruct,

@@ -8,7 +8,8 @@

 # "--disable-maintainer-mode" argument passed in src/Makefile to the

 # respective configure scripts. This was added to avoid regenerating

 # autotools artifacts on user machines (the timestamp protection fails

-# through svn).

+# through svn). ALSO make sure not to remove the maintainer mode macro call

+# in gstruct|gmap/configure.ac (revert the change from the update).

 ##########################################################

 updateGMAPSrc <- function() {

@@ -13,7 +13,7 @@

 updateGMAPSrc <- function() {

   gmapSVNProj <-

-    "http://resscm/bioinfo/projects/gmap/releases/public-2013-03-31"

+    "http://resscm/bioinfo/projects/gmap/releases/internal-2013-10-01"

   extractDirGmap <- file.path(getwd(), "src/gmap")

   .bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

                        program="gmap", bootstrap = "bootstrap.gsnaptoo")

@@ -1,5 +1,16 @@

 ##run this to update. The current working directory needs to be the

 ##top-level directory of the SVN checkout

+

+#########################################################

+## PLEASE READ

+##########################################################

+# When building a new version of gstruct/gmap, remove the

+# "--disable-maintainer-mode" argument passed in src/Makefile to the

+# respective configure scripts. This was added to avoid regenerating

+# autotools artifacts on user machines (the timestamp protection fails

+# through svn).

+##########################################################

+

 updateGMAPSrc <- function() {

   gmapSVNProj <-

     "http://resscm/bioinfo/projects/gmap/releases/public-2013-03-31"

@@ -2,10 +2,10 @@

 ##top-level directory of the SVN checkout

 updateGMAPSrc <- function() {

   gmapSVNProj <-

-    "http://resscm/bioinfo/projects/gmap/branches/internal-2011-12-28"

+    "http://resscm/bioinfo/projects/gmap/releases/public-2013-03-31"

   extractDirGmap <- file.path(getwd(), "src/gmap")

   .bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

-                       program="gmap")

+                       program="gmap", bootstrap = "bootstrap.gsnaptoo")

 }

 updateGSTRUCTSrc <- function() {

@@ -13,7 +13,8 @@ updateGSTRUCTSrc <- function() {

   extractDirGstruct <- file.path(getwd(), "src/gstruct")

   .bootstrapAndExtract(projectSVNURL=gstructSVNProj,

                        extractDir=extractDirGstruct,

-                       program="gstruct")

+                       program="gstruct",

+                       bootstrap = "bootstrap.Rdist")

   .copySamflagsHeader(extractDirGstruct, file.path(getwd(), "src/gmap"))

 }

@@ -21,7 +22,9 @@ updateGSTRUCTSrc <- function() {

 ###helper functions

 ###################

-.bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

+.bootstrapAndExtract <- function(projectSVNURL, extractDir, program,

+                                 bootstrap.script)

+{

   startingDir <- getwd()

   on.exit(setwd(startingDir))

@@ -33,7 +36,7 @@ updateGSTRUCTSrc <- function() {

   svnCheckoutDir <- .getSVNProj(projectSVNURL, extractDir)

   on.exit(unlink(svnCheckoutDir, recursive=TRUE), add=TRUE)

   setwd(svnCheckoutDir)

-  .bootstrapSVNCheckout()  

+  .bootstrapSVNCheckout(bootstrap.script)  

   .configureSrc(program)

   .makeDist()

   .extractDistTarballIntoSrcDirectory(extractDir)

@@ -69,8 +72,8 @@ updateGSTRUCTSrc <- function() {

 }

 ##assumes in the correct dir

-.bootstrapSVNCheckout <- function() {

-  if (!system("./bootstrap.Rdist") == 0) {

+.bootstrapSVNCheckout <- function(bootstrap.script) {

+  if (!system(paste0("./", bootstrap.script)) == 0) {

     stop("unable to bootstrap")

   }

 }

@@ -1,17 +1,20 @@

 ##run this to update. The current working directory needs to be the

 ##top-level directory of the SVN checkout

-updateGMAPRSrc <- function() {

-  gmapSVNProj <- "http://resscm/bioinfo/projects/gmap/branches/internal-2011-12-28"

-  gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

-

+updateGMAPSrc <- function() {

+  gmapSVNProj <-

+    "http://resscm/bioinfo/projects/gmap/branches/internal-2011-12-28"

   extractDirGmap <- file.path(getwd(), "src/gmap")

-  extractDirGstruct <- file.path(getwd(), "src/gstruct")

-

   .bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

-                      program="gmap")  

-  .bootstrapAndExtract(projectSVNURL=gstructSVNProj, extractDir=extractDirGstruct,

-                      program="gstruct")

-  .copySamflagsHeader(extractDirGstruct, extractDirGmap)

+                       program="gmap")

+  

+}

+updateGSTRUCTSrc <- function() {

+  gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

+  extractDirGstruct <- file.path(getwd(), "src/gstruct")

+  .bootstrapAndExtract(projectSVNURL=gstructSVNProj,

+                       extractDir=extractDirGstruct,

+                       program="gstruct")

+  .copySamflagsHeader(extractDirGstruct, file.path(getwd(), "src/gmap"))

 }

 ###################

@@ -7,14 +7,18 @@ updateGMAPRSrc <- function() {

   extractDirGmap <- file.path(getwd(), "src/gmap")

   extractDirGstruct <- file.path(getwd(), "src/gstruct")

-  bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

+  .bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

                       program="gmap")  

-  bootstrapAndExtract(projectSVNURL=gstructSVNProj, extractDir=extractDirGstruct,

+  .bootstrapAndExtract(projectSVNURL=gstructSVNProj, extractDir=extractDirGstruct,

                       program="gstruct")

   .copySamflagsHeader(extractDirGstruct, extractDirGmap)

 }

-  

-bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

+

+###################

+###helper functions

+###################

+

+.bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

   startingDir <- getwd()

   on.exit(setwd(startingDir))

@@ -33,10 +37,6 @@ bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

   invisible(TRUE)

 }

-###################

-###helper functions

-###################

-

 .copySamflagsHeader <- function(extractDirGstruct, extractDirGmap) {

   ##gstruct needs samflags.h. Copying from the gmap src

   gstructSamflagsLoc <- file.path(extractDirGstruct, "src/samflags.h")

@@ -18,6 +18,11 @@ bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

   startingDir <- getwd()

   on.exit(setwd(startingDir))

+  if (file.exists(extractDir)) {

+    unlink(extractDir, recursive=TRUE)

+  }

+  dir.create(extractDir)

+  

   svnCheckoutDir <- .getSVNProj(projectSVNURL, extractDir)

   on.exit(unlink(svnCheckoutDir, recursive=TRUE), add=TRUE)

   setwd(svnCheckoutDir)

@@ -67,7 +72,6 @@ bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

   }

 }

-

 .configureSrc <- function(program) {

   ##--with-gmapdb=${GMAPDB} --prefix=${PREFIX}

   ##configure. Set

@@ -1,26 +1,74 @@

-bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

+##run this to update. The current working directory needs to be the

+##top-level directory of the SVN checkout

+updateGMAPRSrc <- function() {

+  gmapSVNProj <- "http://resscm/bioinfo/projects/gmap/branches/internal-2011-12-28"

+  gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

+

+  extractDirGmap <- file.path(getwd(), "src/gmap")

+  extractDirGstruct <- file.path(getwd(), "src/gstruct")

+  bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

+                      program="gmap")  

+  bootstrapAndExtract(projectSVNURL=gstructSVNProj, extractDir=extractDirGstruct,

+                      program="gstruct")

+  .copySamflagsHeader(extractDirGstruct, extractDirGmap)

+}

+  

+bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

   startingDir <- getwd()

   on.exit(setwd(startingDir))

-  

+

+  svnCheckoutDir <- .getSVNProj(projectSVNURL, extractDir)

+  on.exit(unlink(svnCheckoutDir, recursive=TRUE), add=TRUE)

+  setwd(svnCheckoutDir)

+  .bootstrapSVNCheckout()  

+  .configureSrc(program)

+  .makeDist()

+  .extractDistTarballIntoSrcDirectory(extractDir)

+  invisible(TRUE)

+}

+

+###################

+###helper functions

+###################

+

+.copySamflagsHeader <- function(extractDirGstruct, extractDirGmap) {

+  ##gstruct needs samflags.h. Copying from the gmap src

+  gstructSamflagsLoc <- file.path(extractDirGstruct, "src/samflags.h")

+  if (!file.exists(gstructSamflagsLoc)) {

+    

+    gmapSamflagsLoc <- file.path(extractDirGmap, "src/samflags.h")  

+    if (!file.exists(gmapSamflagsLoc)) {

+      stop("Could not find the samflags.h file in the gmap src code")

+    }

+    

+    file.copy(gmapSamflagsLoc, gstructSamflagsLoc)

+  }

+}

+

+.getSVNProj <- function(projectSVNURL, extractDir) {

   ##grab from svn

   tmpDir <- file.path(tempdir(), basename(extractDir))

   dir.create(tmpDir, recursive=TRUE)

-  on.exit(unlink(tmpDir, recursive=TRUE), add=TRUE)

-  

   command <- paste("svn co",

                    projectSVNURL,

                    tmpDir)

   if (!system(command) == 0) {

     stop("Could not check out project from SVN")

   }

-    

-  ##bootstrap it

-  setwd(tmpDir)

+

+  return(tmpDir)

+}

+

+##assumes in the correct dir

+.bootstrapSVNCheckout <- function() {

   if (!system("./bootstrap.Rdist") == 0) {

     stop("unable to bootstrap")

   }

+}

+

+.configureSrc <- function(program) {

   ##--with-gmapdb=${GMAPDB} --prefix=${PREFIX}

   ##configure. Set

   ##run a "make dist" to build a tarball

@@ -37,22 +85,29 @@ bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

       system("touch config.site")

     }

   }

-  

+}

+

+.makeDist <- function() {

   ##run a "make dist" to build a tarball

   if (!system("make distcheck") == 0) {

     stop("unable to 'make dist'")

   }  

-  

+}

+

+.extractDistTarballIntoSrcDirectory <- function(extractDir) {

   ##extract tarball into 'src' directory of package

-  distTarball <- dir(pattern="*\\.tar\\.gz$")

+  distTarball <- dir(pattern="*\\.tar\\.gz$", full.names=TRUE)

   if (length(distTarball) > 1) {

     stop("Found more than one tarball in directory. ",

          "Not sure which is the distribution. Aborting.")

   }

-  if (!file.exists(extractDir)) {

-    dir.create(extractDir, recursive=TRUE)

+  distTarball <- tools::file_path_as_absolute(distTarball)

+  if (file.exists(extractDir)) {

+    unlink(extractDir, recursive=TRUE)

   }

-  distName <- sub("\\..*", "", distTarball)

+  dir.create(extractDir, recursive=TRUE)

+

+  distName <- sub("\\..*", "", basename(distTarball))

   command <- paste("tar xvf", distTarball,

                    "-C",

                    extractDir,

@@ -71,31 +126,4 @@ bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

     stop("Could not move extracted directory down one level")

   }

   unlink(whereTarExtracted, recursive=TRUE)

-

-  invisible(TRUE)

-}

-

-options(error=recover)

-

-gmapSVNProj <- "http://resscm/bioinfo/projects/gmap/branches/internal-2011-12-28"

-extractDirGmap <- file.path(getwd(), "src/gmap")

-bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

-                    program="gmap")

-

-gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

-extractDirGstruct <- file.path(getwd(), "src/gstruct")

-bootstrapAndExtract(projectSVNURL=gstructSVNProj, extractDir=extractDirGstruct,

-                    program="gstruct")

-

-##gstruct needs samflags.h. Copying from the gmap src

-gstructSamflagsLoc <- file.path(extractDirGstruct, "src/samflags.h")

-if (!file.exists(gstructSamflagsLoc)) {

- 

-  gmapSamflagsLoc <- file.path(extractDirGmap, "src/samflags.h")  

-  if (!file.exists(gmapSamflagsLoc)) {

-    stop("Could not find the samflags.h file in the gmap src code")

-  }

-

-  file.copy(gmapSamflagsLoc, gstructSamflagsLoc)

 }

-    

new file mode 100644

@@ -0,0 +1,101 @@

+bootstrapAndExtract <- function(projectSVNURL, extractDir, program) {

+

+  startingDir <- getwd()

+  on.exit(setwd(startingDir))

+  

+  ##grab from svn

+  tmpDir <- file.path(tempdir(), basename(extractDir))

+  dir.create(tmpDir, recursive=TRUE)

+  on.exit(unlink(tmpDir, recursive=TRUE), add=TRUE)

+  

+  command <- paste("svn co",

+                   projectSVNURL,

+                   tmpDir)

+  if (!system(command) == 0) {

+    stop("Could not check out project from SVN")

+  }

+    

+  ##bootstrap it

+  setwd(tmpDir)

+  if (!system("./bootstrap.Rdist") == 0) {

+    stop("unable to bootstrap")

+  }

+

+  ##--with-gmapdb=${GMAPDB} --prefix=${PREFIX}

+  ##configure. Set

+  ##run a "make dist" to build a tarball

+  command <- "./configure --disable-fulldist"

+  ##if (program == "gstruct") command <- paste(command, "--disable-binaries")

+  if (!system(command) == 0) {

+    stop("unable to configure")

+  }

+

+  ##gstruct SVN repo doesn't have config.site (this code needs to work

+  ##today)

+  if (program == "gstruct") {

+    if (!file.exists("config.site")) {

+      system("touch config.site")

+    }

+  }

+  

+  ##run a "make dist" to build a tarball

+  if (!system("make distcheck") == 0) {

+    stop("unable to 'make dist'")

+  }  

+  

+  ##extract tarball into 'src' directory of package

+  distTarball <- dir(pattern="*\\.tar\\.gz$")

+  if (length(distTarball) > 1) {

+    stop("Found more than one tarball in directory. ",

+         "Not sure which is the distribution. Aborting.")

+  }

+  if (!file.exists(extractDir)) {

+    dir.create(extractDir, recursive=TRUE)

+  }

+  distName <- sub("\\..*", "", distTarball)

+  command <- paste("tar xvf", distTarball,

+                   "-C",

+                   extractDir,

+                   distName)

+  if (!system(command) == 0) {

+    stop("Could not extract source from distribution into specified directory.")

+  }

+

+  ##move contents of untarred dir up one level

+  ##TODO: How (or can) you do this w/ a tar command?

+  whereTarExtracted <- file.path(extractDir, distName)

+  command <- paste("mv",

+                   paste0(whereTarExtracted, "/*"),

+                   extractDir)

+  if (!system(command) == 0) {

+    stop("Could not move extracted directory down one level")

+  }

+  unlink(whereTarExtracted, recursive=TRUE)

+

+  invisible(TRUE)

+}

+

+options(error=recover)

+

+gmapSVNProj <- "http://resscm/bioinfo/projects/gmap/branches/internal-2011-12-28"

+extractDirGmap <- file.path(getwd(), "src/gmap")

+bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

+                    program="gmap")

+

+gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

+extractDirGstruct <- file.path(getwd(), "src/gstruct")

+bootstrapAndExtract(projectSVNURL=gstructSVNProj, extractDir=extractDirGstruct,

+                    program="gstruct")

+

+##gstruct needs samflags.h. Copying from the gmap src

+gstructSamflagsLoc <- file.path(extractDirGstruct, "src/samflags.h")

+if (!file.exists(gstructSamflagsLoc)) {

+ 

+  gmapSamflagsLoc <- file.path(extractDirGmap, "src/samflags.h")  

+  if (!file.exists(gmapSamflagsLoc)) {

+    stop("Could not find the samflags.h file in the gmap src code")

+  }

+

+  file.copy(gmapSamflagsLoc, gstructSamflagsLoc)

+}

+