pyrox.dev
dragmap: init at 1.3.0
Genomic mapper. Open-source version of DRAGEN.
Tests are run during execution with google-tests.
authored by Alexis Praga and committed by Alexis Praga c35f615a da5c2592
+60
pkgs/by-name/dr/dragmap/cstdint.patch
+60
pkgs/by-name/dr/dragmap/cstdint.patch
···
1
+
diff --git a/src/include/map/SeedPosition.hpp b/src/include/map/SeedPosition.hpp
2
+
index 30a7d47..c05af16 100644
3
+
--- a/src/include/map/SeedPosition.hpp
4
+
+++ b/src/include/map/SeedPosition.hpp
5
+
@@ -16,6 +16,7 @@
6
+
#define MAP_SEED_POSITION_HPP
7
+
8
+
#include <ostream>
9
+
+#include <cstdint>
10
+
11
+
#include "sequences/Seed.hpp"
12
+
13
+
diff --git a/src/include/sequences/Read.hpp b/src/include/sequences/Read.hpp
14
+
index 460c1cb..c7ff619 100644
15
+
--- a/src/include/sequences/Read.hpp
16
+
+++ b/src/include/sequences/Read.hpp
17
+
@@ -16,6 +16,7 @@
18
+
#define SEQUENCES_READ_HPP
19
+
20
+
#include <iostream>
21
+
+#include <cstdint>
22
+
#include <string>
23
+
#include <vector>
24
+
25
+
diff --git a/src/include/sequences/Seed.hpp b/src/include/sequences/Seed.hpp
26
+
index a242153..dd4d23b 100644
27
+
--- a/src/include/sequences/Seed.hpp
28
+
+++ b/src/include/sequences/Seed.hpp
29
+
@@ -16,6 +16,7 @@
30
+
#define SEQUENCES_SEED_HPP
31
+
32
+
#include <ostream>
33
+
+#include <cstdint>
34
+
#include <vector>
35
+
36
+
#include "sequences/Read.hpp"
37
+
diff --git a/src/lib/sequences/tests/unit/CrcHasherMocks.hpp b/src/lib/sequences/tests/unit/CrcHasherMocks.hpp
38
+
index 1866be7..5d9b7d7 100644
39
+
--- a/src/lib/sequences/tests/unit/CrcHasherMocks.hpp
40
+
+++ b/src/lib/sequences/tests/unit/CrcHasherMocks.hpp
41
+
@@ -2,6 +2,7 @@
42
+
43
+
#include <array>
44
+
#include <cassert>
45
+
+#include <cstdint>
46
+
#include <cstdlib>
47
+
#include <string>
48
+
49
+
diff --git a/stubs/dragen/src/host/dragen_api/read_group_list.hpp b/stubs/dragen/src/host/dragen_api/read_group_list.hpp
50
+
index eefb9ae..623a77f 100644
51
+
--- a/stubs/dragen/src/host/dragen_api/read_group_list.hpp
52
+
+++ b/stubs/dragen/src/host/dragen_api/read_group_list.hpp
53
+
@@ -14,6 +14,7 @@
54
+
#define __READ_GROUP_LIST_HPP__
55
+
56
+
#include "dragen_exception.hpp"
57
+
+#include <cstdint>
58
+
class ReadGroupList {
59
+
public:
60
+
const std::string &getReadGroupName(const uint16_t idx) const {
+68
pkgs/by-name/dr/dragmap/package.nix
+68
pkgs/by-name/dr/dragmap/package.nix
···
1
+
{
2
+
lib,
3
+
stdenv,
4
+
fetchFromGitHub,
5
+
boost,
6
+
gtest,
7
+
zlib,
8
+
}:
9
+
10
+
stdenv.mkDerivation (finalAttrs: {
11
+
pname = "dragmap";
12
+
version = "1.3.0";
13
+
14
+
src = fetchFromGitHub {
15
+
owner = "Illumina";
16
+
repo = "DRAGMAP";
17
+
rev = finalAttrs.version;
18
+
fetchSubmodules = true;
19
+
hash = "sha256-f1jsOErriS1I/iUS4CzJ3+Dz8SMUve/ccb3KaE+L7U8=";
20
+
};
21
+
22
+
nativebuildInputs = [ boost ];
23
+
buildInputs = [
24
+
gtest
25
+
zlib
26
+
];
27
+
28
+
patches = [
29
+
# pclose is called on a NULL value. This is no longer allowed since
30
+
# https://github.com/bminor/glibc/commit/64b1a44183a3094672ed304532bedb9acc707554
31
+
./stdio-pclose.patch
32
+
33
+
# Add missing include cstdint. Upstream does not accept PR. Issue opened at
34
+
# https://github.com/Illumina/DRAGMAP/issues/63
35
+
./cstdint.patch
36
+
];
37
+
38
+
env = {
39
+
GTEST_INCLUDEDIR = "${gtest.dev}/include";
40
+
CPPFLAGS = "-I ${boost.dev}/include";
41
+
LDFLAGS = "-L ${boost.out}/lib";
42
+
};
43
+
44
+
installPhase = ''
45
+
runHook preInstall
46
+
47
+
mkdir -p $out/bin
48
+
cp build/release/dragen-os $out/bin/
49
+
50
+
runHook postInstall
51
+
'';
52
+
53
+
# Tests are launched by default from makefile
54
+
doCheck = false;
55
+
56
+
meta = with lib; {
57
+
description = "Open Source version of Dragen mapper for genomics";
58
+
mainProgram = "dragen-os";
59
+
longDescription = ''
60
+
DRAGMAP is an open-source software implementation of the DRAGEN mapper,
61
+
which the Illumina team created to procude the same results as their
62
+
proprietary DRAGEN hardware.
63
+
'';
64
+
license = licenses.gpl3;
65
+
platforms = platforms.unix;
66
+
maintainers = with maintainers; [ apraga ];
67
+
};
68
+
})
+12
pkgs/by-name/dr/dragmap/stdio-pclose.patch
+12
pkgs/by-name/dr/dragmap/stdio-pclose.patch
···
1
+
diff --git a/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp b/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
2
+
index cd02cd4..c26e9cf 100644
3
+
--- a/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
4
+
+++ b/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
5
+
@@ -57,7 +57,6 @@ int GetDmiValue(const std::string& label, std::string& value)
6
+
FILE* dmiOutput = popen("sudo /usr/sbin/dmidecode -t 2", "r");
7
+
if (dmiOutput == NULL) {
8
+
perror("dmidecode popen");
9
+
- pclose(dmiOutput);
10
+
return -1;
11
+
}
12
+