scan

.gitignore

@@ -14,3 +14,4 @@ script/Makefile
 script/Makefile.in
 aclocal.m4
 config.h
+bazel-*

BUILD

@@ -1,51 +1,276 @@
+
 cc_library(
-    name = "assembly",
-    srcs = glob(
-        [
-          "src/basic/*.cpp",
-          "src/container/*.cpp",
-          "src/sequence/*.cpp",
-          "src/graph/*.cpp",
-          "src/misc/*.cpp",
-          "src/assembly/*.cpp"
-        ]
-    ),
-    hdrs = glob(
-        [
-          "src/basic/*.h",
-          "src/container/*.h",
-          "src/sequence/*.h",
-          "src/graph/*.h",
-          "src/misc/*.h",
-          "src/assembly/*.h"
-        ]
-    ),
-    includes = ["src"],
-    copts = ["-Wall", "-O3", "-fopenmp"],
+  name = "assembly",
+  srcs = glob(
+    [
+      "src/basic/*.cpp",
+      "src/container/*.cpp",
+      "src/sequence/*.cpp",
+      "src/graph/*.cpp",
+      "src/misc/*.cpp",
+      "src/assembly/*.cpp"
+    ]
+  ),
+  hdrs = glob(
+    [
+      "src/basic/*.h",
+      "src/container/*.h",
+      "src/sequence/*.h",
+      "src/graph/*.h",
+      "src/misc/*.h",
+      "src/assembly/*.h"
+    ]
+  ),
+  includes = ["src"],
+  copts = ["-Wall", "-O3", "-fopenmp"],
 )
 
 cc_test(
-    name = "unit_test",
-    srcs = glob(["src/test/*.cpp", "gtest_src/gtest/*.cc", "gtest_src/gtest/*.h"]),
-    includes = ["gtest_src", "src"],
-    copts = ["-Wall", "-O3", "-fopenmp"],
-    linkopts = ["-pthread", "-fopenmp", "-lm"],
-    deps = [":assembly"],
+  name = "unit_test",
+  srcs = glob(["src/test/*.cpp", "gtest_src/gtest/*.cc", "gtest_src/gtest/*.h"]),
+  includes = ["gtest_src", "src"],
+  copts = ["-Wall", "-O3", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+
+cc_binary(
+  name = "filterfa",
+  srcs = ["src/release/filterfa.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "fq2fa",
+  srcs = ["src/release/fq2fa.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "idba",
+  srcs = ["src/release/idba.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
 )
 
 cc_binary(
-    name = "idba",
-    srcs = ["src/release/idba.cpp"],
-    copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
-    linkopts = ["-pthread", "-fopenmp", "-lm"],
-    deps = [":assembly"],
+  name = "idba_hybrid",
+  srcs = ["src/release/idba_hybrid.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
 )
 
 cc_binary(
-    name = "idba_ud",
-    srcs = ["src/release/idba_ud.cpp"],
-    copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
-    linkopts = ["-pthread", "-fopenmp", "-lm"],
-    deps = [":assembly"],
+  name = "idba_tran",
+  srcs = ["src/release/idba_tran.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
 )
 
+cc_binary(
+  name = "idba_ud",
+  srcs = ["src/release/idba_ud.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "parallel_blat",
+  srcs = ["src/release/parallel_blat.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "raw_n50",
+  srcs = ["src/release/raw_n50.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "sim_reads",
+  srcs = ["src/release/sim_reads.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "sim_reads_tran",
+  srcs = ["src/release/sim_reads_tran.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "split_scaffold",
+  srcs = ["src/release/split_scaffold.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "validate_contigs_blat",
+  srcs = ["src/release/validate_contigs_blat.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "fa2fq",
+  srcs = ["src/tools/fa2fq.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "filter_blat",
+  srcs = ["src/tools/filter_blat.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "filter_contigs",
+  srcs = ["src/tools/filter_contigs.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "idba_tran_test",
+  srcs = ["src/tools/idba_tran_test.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "parallel_rna_blat",
+  srcs = ["src/tools/parallel_rna_blat.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "print_graph",
+  srcs = ["src/tools/print_graph.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "sample_reads",
+  srcs = ["src/tools/sample_reads.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "scaffold",
+  srcs = ["src/tools/scaffold.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "shuffle_reads",
+  srcs = ["src/tools/shuffle_reads.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "sort_psl",
+  srcs = ["src/tools/sort_psl.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "sort_reads",
+  srcs = ["src/tools/sort_reads.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "split_fa",
+  srcs = ["src/tools/split_fa.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "split_fq",
+  srcs = ["src/tools/split_fq.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "test",
+  srcs = ["src/tools/test.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "validate_component",
+  srcs = ["src/tools/validate_component.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "validate_contigs_mummer",
+  srcs = ["src/tools/validate_contigs_mummer.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "validate_reads_blat",
+  srcs = ["src/tools/validate_reads_blat.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)
+
+cc_binary(
+  name = "validate_rna",
+  srcs = ["src/tools/validate_rna.cpp"],
+  copts = ["-Wall", "-O3", "-Isrc", "-fopenmp"],
+  linkopts = ["-pthread", "-fopenmp", "-lm"],
+  deps = [":assembly"],
+)

Dockerfile

@@ -1,6 +1,11 @@
-FROM ubuntu:14.04
+FROM ubuntu:15.10
 MAINTAINER Yu Peng <[email protected]>
-RUN apt-get update && apt-get install -y gcc autoconf automake g++ make
+RUN apt-get update
+RUN apt-get install -y openjdk-8-jdk
+RUN apt-get install -y pkg-config zip g++ zlib1g-dev unzip bash-completion wget
+RUN apt-get install -y gcc autoconf automake g++ make
+RUN wget https://github.com/bazelbuild/bazel/releases/download/0.2.0/bazel_0.2.0-linux-x86_64.deb
+RUN dpkg -i bazel_0.2.0-linux-x86_64.deb
 ADD . /root/idba
-RUN cd /root/idba && ./build.sh
-ENV PATH=${PATH}:/root/idba/bin/
+RUN apt-get install -y vim
+RUN cd /root/idba && bazel build //:*