update the sources url

Author: Miachol

ChangeLog

@@ -1,3 +1,8 @@
+2018-11-13 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
+
+		* change samtools and htslib source_url t codeload
+		* add the second source url of gridss 
+
 2018-11-11 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
 
 		* improve the sort method of versions

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioInstaller
 Title: Integrator of Bioinformatics Resources
-Version: 0.3.6.3000
+Version: 0.3.6.3001
 Authors@R: person("Jianfeng", "Li", email = "lee_jianfeng@sjtu.edu.cn", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2349-208X"))
 Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
 Description:

R/versions.R

@@ -11,7 +11,7 @@ get.github.version <- function(config) {
   }
   result <- str_sort(result, numeric = TRUE)
   if (!("master" %in% result)) {
-    result <- c(result, "master")
+    result <- c("master", result)
   }
   black_list <- c("vcf-direct-final", "stable2", "stable1", "konnector2-prerelease", 
     "konnector-prelease", "bc_4.13", "BCM", "st-final", "sgdp")

inst/extdata/config/nongithub/nongithub.toml

@@ -485,7 +485,7 @@ linux = "make"
 mac = "make"
 
 [htslib]
-source_url = "https://github.com/samtools/htslib/archive/{{version}}.tar.gz"
+source_url = "https://codeload.github.com/samtools/htslib/tar.gz/{{version}}"
 use_github_versions = true
 after_success = ["ln -s htslib/* ./; echo successful!"]
 make_dir = ["./"]
@@ -496,7 +496,7 @@ linux = ["autoheader; autoconf; ./configure --prefix={{destdir}}; make;", " make
 mac = ["autoheader; autoconf; ./configure --prefix={{destdir}}; make;", " make install"]
 
 [samtools]
-source_url = "https://github.com/samtools/samtools/archive/{{version}}.tar.gz"
+source_url = "https://codeload.github.com/samtools/samtools/tar.gz/{{version}}"
 use_github_versions = true
 dependence = ["htslib"]
 dependence_version = ["{{version}}"]
@@ -660,7 +660,8 @@ win = ["ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{{version}}/ncbi-bla
        "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{{version}}/ncbi-blast-{{version}}+-win64.exe"]
 
 [gridss]
-source_url = "https://github.com/PapenfussLab/gridss/releases/download/{{version}}/gridss-@>@str_replace('{{version}}', 'v', '')@<@-jar-with-dependencies.jar"
+source_url = ["https://github.com/PapenfussLab/gridss/releases/download/{{version}}/gridss-@>@str_replace('{{version}}', 'v', '')@<@-jar-with-dependencies.jar", 
+             "https://github.com/PapenfussLab/gridss/releases/download/{{version}}/gridss-@>@str_replace('{{version}}', 'v', '')@<@-gridss-jar-with-dependencies.jar"]
 use_github_versions = true
 [gridss.install]
 linux = "mkdir -p {{destdir}}/bin; cp {{download.dir}}/*.jar {{destdir}}/bin"