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-rw-r--r--var/spack/repos/builtin/packages/ncbi-toolkit/package.py15
1 files changed, 15 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py
index 471c95a566..b05530be1c 100644
--- a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py
@@ -14,6 +14,13 @@ class NcbiToolkit(AutotoolsPackage):
homepage = "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/"
url = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--22_0_0.tar.gz"
+ # Per https://ncbi.github.io/cxx-toolkit/pages/ch_getcode_svn#ch_getcode_svn.external
+ # New versions are released on github
+ version(
+ "26_0_1",
+ sha256="aba79da5c8d0407ffc92b7831f4f8f8a8096a15e47a016ada81b6568f9d280cc",
+ url="https://github.com/ncbi/ncbi-cxx-toolkit-public/archive/refs/tags/release-26.0.1.tar.gz",
+ )
version(
"25_2_0",
sha256="9f824a92750e64e7b9be98d82b84414ab4f7e5d73392dadbb87c94ff5ccf9111",
@@ -34,6 +41,8 @@ class NcbiToolkit(AutotoolsPackage):
depends_on("boost@1.35.0:+test+log")
depends_on("bzip2")
+ depends_on("cpio", type="build")
+ depends_on("diffutils", type="build")
depends_on("jpeg")
depends_on("libpng")
depends_on("libtiff")
@@ -46,6 +55,7 @@ class NcbiToolkit(AutotoolsPackage):
depends_on("zlib")
depends_on("samtools")
depends_on("bamtools")
+ depends_on("berkeley-db")
def configure_args(self):
args = ["--without-sybase", "--without-fastcgi"]
@@ -88,6 +98,11 @@ class NcbiToolkit(AutotoolsPackage):
)
filter_file(r"(log_build_info\(ostr)\)", r"\1, true)", file_)
+ with working_dir(join_path("scripts", "common", "impl")):
+ files = ["if_diff.sh", "update_configurable.sh"]
+ for file in files:
+ filter_file("PATH=/bin:/usr/bin", "", file)
+
def build(self, spec, prefix):
with working_dir(join_path(glob("*MT64")[0], "build")):
make("all_r")