Add genodsp (#51488)

* adding genodsp -- General workbench for processing signals along genomic intervals * adding run_exports * sentralized safe_strncpy, using install * forcing null-termination of string * added rependency on stdlib('c') * adding license_file * Update meta.yaml * Update recipes/genodsp/meta.yaml * removing hardcoded gcc in the Makefile * updating safe_strncpy --------- Co-authored-by: Richard C. Burhans <[email protected]> Co-authored-by: Björn Grüning <[email protected]>
bioconda · Oct 22, 2024 · b3727f2 · b3727f2
1 parent 09c5347
commit b3727f2
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diff --git a/recipes/genodsp/build.sh b/recipes/genodsp/build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash -e
+set -uex
+
+mkdir -vp "${PREFIX}/bin"
+
+make VERBOSE=1 -j ${CPU_COUNT}
+
+if ! install -v "$SRC_DIR/genodsp" "$PREFIX/bin/genodsp"; then
+    echo "Failed to install genodsp binary" >&2
+    exit 1
+fi
diff --git a/recipes/genodsp/meta.yaml b/recipes/genodsp/meta.yaml
@@ -0,0 +1,36 @@
+{% set name = "genodsp" %}
+{% set version = "0.0.3" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/rsharris/genodsp/archive/refs/tags/v{{ version }}+.zip
+  sha256: a7fb2218311d1ae5231041863d28adb8b5fffe724fc5ff2422310ce90a9f894a
+  patches:
+    - stringop-truncation.patch
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - make
+
+build:
+  number: 0
+  skip: True  # [not linux or not x86_64]
+  run_exports:
+    - {{ pin_subpackage('genodsp', max_pin="x.x") }}
+
+test:
+  commands:
+    - genodsp --help
+    - ls -l ${PREFIX}/bin/
+    - ${PREFIX}/bin/genodsp --help 
+
+about:
+  home: https://github.com/rsharris/genodsp
+  summary: General workbench for processing signals along genomic (chromosomal) intervals
+  license: GPL-3.0-only
+  license_file: LICENSE
+  license_url: https://github.com/rsharris/genodsp/blob/master/LICENSE
diff --git a/recipes/genodsp/stringop-truncation.patch b/recipes/genodsp/stringop-truncation.patch
@@ -0,0 +1,185 @@
+diff --git a/Makefile b/Makefile
+index cf07368..d1dfb95 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,4 @@
+ CFLAGS = -O3 -Wall -Wextra -Werror
+-CC     = gcc
+ LDLIBS = -lm
+
+ operators = sum clump percentile add multiply mask logical minmax morphology map opio variables
+diff --git a/add.c b/add.c
+index 752dd5d..8fa4bad 100644
+--- a/add.c
++++ b/add.c
+@@ -240,7 +240,7 @@ void op_add_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		if (chromSpec == NULL) continue;
+@@ -533,7 +533,7 @@ void op_subtract_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		if (chromSpec == NULL) continue;
+diff --git a/genodsp.c b/genodsp.c
+index ac1704e..dffd622 100644
+--- a/genodsp.c
++++ b/genodsp.c
+@@ -1229,7 +1229,7 @@ void read_intervals
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		if (chromSpec == NULL) continue;
+diff --git a/logical.c b/logical.c
+index fb295e3..45e1c20 100644
+--- a/logical.c
++++ b/logical.c
+@@ -497,7 +497,7 @@ void op_or_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		if (chromSpec == NULL) continue;
+@@ -810,7 +810,7 @@ void op_and_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		// if the current chromosome is not of any interest, ignore this
+diff --git a/mask.c b/mask.c
+index 4fd5ebd..ddd068e 100644
+--- a/mask.c
++++ b/mask.c
+@@ -253,7 +253,7 @@ void op_mask_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		if (chromSpec == NULL) continue;
+@@ -548,7 +548,7 @@ void op_mask_not_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		// if the current chromosome is not of any interest, ignore this
+diff --git a/minmax.c b/minmax.c
+index c222bd0..eae69ab 100644
+--- a/minmax.c
++++ b/minmax.c
+@@ -261,7 +261,7 @@ void op_min_in_interval_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		// if the current chromosome is not of any interest, ignore this
+@@ -664,7 +664,7 @@ void op_max_in_interval_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		// if the current chromosome is not of any interest, ignore this
+@@ -1941,7 +1941,7 @@ void op_min_with_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		if (chromSpec == NULL) continue;
+@@ -2227,7 +2227,7 @@ void op_max_with_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		if (chromSpec == NULL) continue;
+diff --git a/multiply.c b/multiply.c
+index 4c1b550..d04cc41 100644
+--- a/multiply.c
++++ b/multiply.c
+@@ -260,7 +260,7 @@ void op_multiply_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		// if the current chromosome is not of any interest, ignore this
+@@ -654,7 +654,7 @@ void op_divide_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+
+ 		// if the current chromosome is not of any interest, ignore this
+diff --git a/utilities.c b/utilities.c
+index 03d2ff1..3157538 100644
+--- a/utilities.c
++++ b/utilities.c
+@@ -493,3 +493,16 @@ char* ucommatize
+ 	return s;
+ 	}
+
++//
++void safe_strncpy
++   (char *dest, const char *src, size_t n)
++    {
++    #pragma GCC diagnostic push
++    #pragma GCC diagnostic ignored "-Wstringop-truncation"
++    strncpy(dest, src, n);
++    #pragma GCC diagnostic pop
++    if (n > 0)
++        {
++        dest[n-1] = '\0';  // Ensure null-termination
++        }
++    }
+diff --git a/utilities.h b/utilities.h
+index ac9cef7..87cfc2d 100644
+--- a/utilities.h
++++ b/utilities.h
+@@ -31,6 +31,8 @@ char*  skip_whitespace        (char* s);
+ char*  skip_darkspace         (char* s);
+ char*  duration_to_string     (float seconds);
+ char*  ucommatize             (const u32 v);
++void   safe_strncpy           (char *dest, const char *src, size_t n);
++
+
+ // miscellany
+