From 7acfc7a62c4b8fa215f4d22dff73254f04dca4a5 Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Fri, 13 Dec 2024 15:38:03 +0200 Subject: [PATCH 01/11] Add recipe for softsv Signed-off-by: Martin Tzvetanov Grigorov --- recipes/softsv/build.sh | 10 ++++++++ recipes/softsv/makefile.patch | 13 +++++++++++ recipes/softsv/meta.yaml | 43 +++++++++++++++++++++++++++++++++++ 3 files changed, 66 insertions(+) create mode 100644 recipes/softsv/build.sh create mode 100644 recipes/softsv/makefile.patch create mode 100644 recipes/softsv/meta.yaml diff --git a/recipes/softsv/build.sh b/recipes/softsv/build.sh new file mode 100644 index 0000000000000..217a7aa6ed8cb --- /dev/null +++ b/recipes/softsv/build.sh @@ -0,0 +1,10 @@ +#!/usr/bin/env bash + +set -xe + +CXX="${CXX} -std=c++14" make -j"${CPU_COUNT}" + +ls -la + +mkdir -p ${PREFIX}/bin +install -m 755 softsv ${PREFIX}/bin diff --git a/recipes/softsv/makefile.patch b/recipes/softsv/makefile.patch new file mode 100644 index 0000000000000..e6125c5cc4302 --- /dev/null +++ b/recipes/softsv/makefile.patch @@ -0,0 +1,13 @@ +diff --git i/Makefile w/Makefile +index de28bc8..e352ed0 100644 +--- i/Makefile ++++ w/Makefile +@@ -6,7 +6,7 @@ SRCS := $(shell find $(SRC_DIR) -type f -name *.cpp) + OBJS := $(patsubst $(SRC_DIR)/%,$(BUILD_DIR)/%,$(SRCS:.cpp=.o)) + + # Compiler +-CXX = g++ -std=c++14 ++CXX ?= g++ -std=c++14 + CC = $(CXX) + + # SeqAn diff --git a/recipes/softsv/meta.yaml b/recipes/softsv/meta.yaml new file mode 100644 index 0000000000000..7920bbec6f4ba --- /dev/null +++ b/recipes/softsv/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "softsv" %} +{% set version = "1.4.2" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +source: + url: https://sourceforge.net/projects/{{ name }}/files/SoftSV_{{ version }}.zip + sha256: b3caea962569f7c30f1257ad148fd1e833f8d0737105b9983579d91da2bed6e8 + patches: + - softsv.patch + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + - boost-cpp + - bamtools + - seqan + +test: + commands: + - ls -la # temporary + +about: + home: https://sourceforge.net/projects/softsv + license: GPL-3.0-only + license_family: GPL3 + license_file: license.txt + summary: SoftSV is a tool for the detection of small and large deletions, inversions, tandem duplications and translocations from paired-end sequencing data. + doc_url: https://sourceforge.net/projects/softsv + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 \ No newline at end of file From c5b47cf985c4357dbb883bcfb0c2b7a0b9a42fee Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 13 Dec 2024 19:17:24 +0200 Subject: [PATCH 02/11] correct patch file name --- recipes/softsv/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/softsv/meta.yaml b/recipes/softsv/meta.yaml index 7920bbec6f4ba..e6b2b2c699d31 100644 --- a/recipes/softsv/meta.yaml +++ b/recipes/softsv/meta.yaml @@ -14,7 +14,7 @@ source: url: https://sourceforge.net/projects/{{ name }}/files/SoftSV_{{ version }}.zip sha256: b3caea962569f7c30f1257ad148fd1e833f8d0737105b9983579d91da2bed6e8 patches: - - softsv.patch + - makefile.patch requirements: build: From 582d6a395e2efa5e84dc87e608c89095f4e3e28c Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Fri, 13 Dec 2024 19:27:05 +0200 Subject: [PATCH 03/11] Fix the paths in the patch Signed-off-by: Martin Tzvetanov Grigorov --- recipes/softsv/build.sh | 2 ++ recipes/softsv/makefile.patch | 6 +++--- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/softsv/build.sh b/recipes/softsv/build.sh index 217a7aa6ed8cb..948992a2bc644 100644 --- a/recipes/softsv/build.sh +++ b/recipes/softsv/build.sh @@ -2,6 +2,8 @@ set -xe +cd SoftSV_1.4.2 + CXX="${CXX} -std=c++14" make -j"${CPU_COUNT}" ls -la diff --git a/recipes/softsv/makefile.patch b/recipes/softsv/makefile.patch index e6125c5cc4302..16215250e9e89 100644 --- a/recipes/softsv/makefile.patch +++ b/recipes/softsv/makefile.patch @@ -1,7 +1,7 @@ -diff --git i/Makefile w/Makefile +diff --git i/SoftSV_1.4.2/Makefile w/SoftSV_1.4.2/Makefile index de28bc8..e352ed0 100644 ---- i/Makefile -+++ w/Makefile +--- i/SoftSV_1.4.2/Makefile ++++ w/SoftSV_1.4.2/Makefile @@ -6,7 +6,7 @@ SRCS := $(shell find $(SRC_DIR) -type f -name *.cpp) OBJS := $(patsubst $(SRC_DIR)/%,$(BUILD_DIR)/%,$(SRCS:.cpp=.o)) From 1a6615e25c02254c73172db1b9aa0d2f895d3411 Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Fri, 13 Dec 2024 19:41:46 +0200 Subject: [PATCH 04/11] Use the correct patch file for SoftSV Signed-off-by: Martin Tzvetanov Grigorov --- recipes/softsv/makefile.patch | 13 --- recipes/softsv/meta.yaml | 2 +- recipes/softsv/softsv.patch | 155 ++++++++++++++++++++++++++++++++++ 3 files changed, 156 insertions(+), 14 deletions(-) delete mode 100644 recipes/softsv/makefile.patch create mode 100644 recipes/softsv/softsv.patch diff --git a/recipes/softsv/makefile.patch b/recipes/softsv/makefile.patch deleted file mode 100644 index 16215250e9e89..0000000000000 --- a/recipes/softsv/makefile.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git i/SoftSV_1.4.2/Makefile w/SoftSV_1.4.2/Makefile -index de28bc8..e352ed0 100644 ---- i/SoftSV_1.4.2/Makefile -+++ w/SoftSV_1.4.2/Makefile -@@ -6,7 +6,7 @@ SRCS := $(shell find $(SRC_DIR) -type f -name *.cpp) - OBJS := $(patsubst $(SRC_DIR)/%,$(BUILD_DIR)/%,$(SRCS:.cpp=.o)) - - # Compiler --CXX = g++ -std=c++14 -+CXX ?= g++ -std=c++14 - CC = $(CXX) - - # SeqAn diff --git a/recipes/softsv/meta.yaml b/recipes/softsv/meta.yaml index e6b2b2c699d31..7920bbec6f4ba 100644 --- a/recipes/softsv/meta.yaml +++ b/recipes/softsv/meta.yaml @@ -14,7 +14,7 @@ source: url: https://sourceforge.net/projects/{{ name }}/files/SoftSV_{{ version }}.zip sha256: b3caea962569f7c30f1257ad148fd1e833f8d0737105b9983579d91da2bed6e8 patches: - - makefile.patch + - softsv.patch requirements: build: diff --git a/recipes/softsv/softsv.patch b/recipes/softsv/softsv.patch new file mode 100644 index 0000000000000..6f763e386972e --- /dev/null +++ b/recipes/softsv/softsv.patch @@ -0,0 +1,155 @@ +diff --git i/SoftSV_1.4.2/makefile w/SoftSV_1.4.2/makefile +index da3a2b0..dad1cef 100644 +--- i/SoftSV_1.4.2/makefile ++++ w/SoftSV_1.4.2/makefile +@@ -2,7 +2,7 @@ + + # You may need to modify the following paths: + # 1. The path to your C++ compiler: +-CC=g++ ++CC?=g++ + + # External libraries: + # 2. Please specify the base directory of your BamTools installation. +@@ -22,7 +22,7 @@ SEQAN=/YourPath/seqan + src/%.o: src/%.cpp + @echo 'Building file: $<' + @echo 'Invoking: GCC C++ Compiler' +- $(CC) -I${BAMTOOLS}/include -I${BAMTOOLS}/include/shared -I${SEQAN}/include -O3 -Wall -c -fmessage-length=0 -std=c++0x -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" ++ $(CC) -std=c++14 -I${PREFIX}/include/bamtools -I${PREFIX}/include/bamtools/shared -I${PREFIX}/include -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" + @echo 'Finished building: $<' + @echo ' ' + +@@ -42,7 +42,7 @@ OBJS += \ + SoftSV: $(OBJS) + @echo 'Building target: $@' + @echo 'Invoking: GCC C++ Linker' +- $(CC) -o $@ $(OBJS) -lboost_program_options -lboost_system -lboost_filesystem -lbamtools -L${BAMTOOLS}/lib ++ $(CC) -std=c++14 -o $@ $(OBJS) -lboost_program_options -lboost_system -lboost_filesystem -lbamtools -L${PREFIX}/lib + @echo 'Finished building target: $@' + @echo ' ' + +diff --git i/SoftSV_1.4.2/src/Deletions.cpp w/src/Deletions.cpp +index 8ea7345..d44297d 100644 +--- i/SoftSV_1.4.2/src/Deletions.cpp ++++ w/src/Deletions.cpp +@@ -20,6 +20,8 @@ + * @date 2015/09/09 + */ + ++#include ++ + #include "Deletions.hpp" + + void Deletions::detection ( const std::string& outputFile, const std::string& outputFile_insertion, BamTools::BamReader& reader, bool verbose ){ +@@ -119,7 +121,7 @@ void Deletions::buildGraph_edges(){ + && + scGraph[read2].is5primeBp != scGraph[read2].scIs5primeBp + && +- abs(scGraph[read1].scPos - scGraph[read2].scPos) <= scBPtol ++ std::abs(scGraph[read1].scPos - scGraph[read2].scPos) <= scBPtol + ) + { + scMatch = softClipsMatch(scGraph[read1].scSeq, scGraph[read2].scSeq); +@@ -141,7 +143,7 @@ void Deletions::buildGraph_edges(){ + scGraph[read2].scPos < (scGraph[read1].scPos + scGraph[read1].scLength) + ){ + +- int scDist = abs(scGraph[read2].scPos - scGraph[read1].scPos) + 1; ++ int scDist = std::abs(scGraph[read2].scPos - scGraph[read1].scPos) + 1; + if(scDist >= 5){ + std::string interScSeq1 = scGraph[read1].scSeq.substr(0, scDist); + std::string interScSeq2 = scGraph[read2].scSeq.substr(scGraph[read2].scLength - scDist, scDist); +@@ -211,7 +213,7 @@ std::string Deletions::generateOutput(const rangeDef& sv, BamTools::BamReader& r + uint medianBpPos1 = medianBp1.first; + uint medianBpPos2 = medianBp2.first; + +- uint svSize = abs(medianBpPos2-(medianBpPos1+1))+1; ++ uint svSize = std::abs((int) (medianBpPos2-(medianBpPos1+1)))+1; + + std::stringstream output, bpSeq; + +diff --git i/SoftSV_1.4.2/src/Inversions.cpp w/src/Inversions.cpp +index 207a774..ff4f8d9 100644 +--- i/SoftSV_1.4.2/src/Inversions.cpp ++++ w/src/Inversions.cpp +@@ -20,6 +20,8 @@ + * @date 2015/09/09 + */ + ++#include ++ + #include "Inversions.hpp" + + // seqaln +@@ -111,7 +113,7 @@ void Inversions::buildGraph_edges(){ + && + scGraph[read1].scIs5primeBp == scGraph[read2].scIs5primeBp + && +- abs(scGraph[read1].scPos - scGraph[read2].scPos) <= scBPtol ++ std::abs(scGraph[read1].scPos - scGraph[read2].scPos) <= scBPtol + ) + { + scMatch = softClipsMatch(scGraph[read1].scSeq, scGraph[read2].scSeq); +@@ -127,7 +129,7 @@ void Inversions::buildGraph_edges(){ + && + scGraph[read1].scIs5primeBp != scGraph[read2].scIs5primeBp + && +- abs(scGraph[read1].scPos - scGraph[read2].scPos) <= scBPtol ) ++ std::abs(scGraph[read1].scPos - scGraph[read2].scPos) <= scBPtol ) + { + scMatch = true; + weight = edgeWeight4; +@@ -255,7 +257,7 @@ std::string Inversions::generateOutput(const rangeDef& sv, BamTools::BamReader& + bpSeq2 << ""; + } + +- uint svSize = abs(medianBpPos2-(medianBpPos1+1))+1; ++ uint svSize = std::abs((int) (medianBpPos2-(medianBpPos1+1)))+1; + + // Outpu format: + // Chr Start End Support(PE) Support(SC) Upstream-breakpoint-sequence Downstream-breakpoint-sequence +diff --git i/SoftSV_1.4.2/src/Misc.cpp w/src/Misc.cpp +index bd10001..e0b460a 100644 +--- i/SoftSV_1.4.2/src/Misc.cpp ++++ w/src/Misc.cpp +@@ -32,6 +32,8 @@ + + // Misc. basics + #include ++#include ++#include + + /** + * @brief Returns the total length of small deletions within the CIGAR string of an alignment. +diff --git i/SoftSV_1.4.2/src/Tandems.cpp w/src/Tandems.cpp +index e6546af..7af0834 100644 +--- i/SoftSV_1.4.2/src/Tandems.cpp ++++ w/src/Tandems.cpp +@@ -20,6 +20,8 @@ + * @date 2015/09/09 + */ + ++#include ++ + #include "Tandems.hpp" + + +@@ -107,7 +109,7 @@ void Tandems::buildGraph_edges(){ + && + scGraph[read2].is5primeBp == scGraph[read2].scIs5primeBp + && +- abs(scGraph[read1].scPos - scGraph[read2].scPos) <= scBPtol ++ std::abs(scGraph[read1].scPos - scGraph[read2].scPos) <= scBPtol + ) + { + scMatch = softClipsMatch(scGraph[read1].scSeq, scGraph[read2].scSeq); +@@ -174,7 +176,7 @@ std::string Tandems::generateOutput(const rangeDef& sv, BamTools::BamReader& rea + uint medianBpPos1 = medianBp1.first; + uint medianBpPos2 = medianBp2.first; + +- uint svSize = abs(medianBpPos2-(medianBpPos1+1))+1; ++ uint svSize = std::abs((int) (medianBpPos2-(medianBpPos1+1)))+1; + + std::stringstream output, bpSeq; + From ffbb0905a5b1bd78666f716af69999cd1756f688 Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Fri, 13 Dec 2024 20:01:21 +0200 Subject: [PATCH 05/11] debug Signed-off-by: Martin Tzvetanov Grigorov --- recipes/softsv/build.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/softsv/build.sh b/recipes/softsv/build.sh index 948992a2bc644..565e8eb9a9416 100644 --- a/recipes/softsv/build.sh +++ b/recipes/softsv/build.sh @@ -2,6 +2,8 @@ set -xe +ls -la + cd SoftSV_1.4.2 CXX="${CXX} -std=c++14" make -j"${CPU_COUNT}" From 03e6bac20f3027aafc1fae6b2781ac03ebbc3544 Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Fri, 13 Dec 2024 20:19:03 +0200 Subject: [PATCH 06/11] No need to cd Signed-off-by: Martin Tzvetanov Grigorov --- recipes/softsv/build.sh | 4 ---- 1 file changed, 4 deletions(-) diff --git a/recipes/softsv/build.sh b/recipes/softsv/build.sh index 565e8eb9a9416..217a7aa6ed8cb 100644 --- a/recipes/softsv/build.sh +++ b/recipes/softsv/build.sh @@ -2,10 +2,6 @@ set -xe -ls -la - -cd SoftSV_1.4.2 - CXX="${CXX} -std=c++14" make -j"${CPU_COUNT}" ls -la From 2b5a1c21a952b379775c14f5fe8ca7d8dd81bc2a Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Fri, 13 Dec 2024 20:31:48 +0200 Subject: [PATCH 07/11] Use SeqAn 2.1.1 Signed-off-by: Martin Tzvetanov Grigorov --- recipes/softsv/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/softsv/meta.yaml b/recipes/softsv/meta.yaml index 7920bbec6f4ba..3877c90cbd01d 100644 --- a/recipes/softsv/meta.yaml +++ b/recipes/softsv/meta.yaml @@ -23,7 +23,7 @@ requirements: host: - boost-cpp - bamtools - - seqan + - seqan ==2.1.1 test: commands: From 03690b79e657bc4b3e655cc6d4aa1782bb216b12 Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Fri, 13 Dec 2024 21:56:33 +0200 Subject: [PATCH 08/11] Add `-Wl,--copy-dt-needed-entries` for the linker https://stackoverflow.com/a/55086637/497381 Signed-off-by: Martin Tzvetanov Grigorov --- recipes/softsv/softsv.patch | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/recipes/softsv/softsv.patch b/recipes/softsv/softsv.patch index 6f763e386972e..1cde2667aca13 100644 --- a/recipes/softsv/softsv.patch +++ b/recipes/softsv/softsv.patch @@ -1,5 +1,5 @@ diff --git i/SoftSV_1.4.2/makefile w/SoftSV_1.4.2/makefile -index da3a2b0..dad1cef 100644 +index da3a2b0..0294964 100644 --- i/SoftSV_1.4.2/makefile +++ w/SoftSV_1.4.2/makefile @@ -2,7 +2,7 @@ @@ -7,7 +7,7 @@ index da3a2b0..dad1cef 100644 # You may need to modify the following paths: # 1. The path to your C++ compiler: -CC=g++ -+CC?=g++ ++CXX?=g++ # External libraries: # 2. Please specify the base directory of your BamTools installation. @@ -16,7 +16,7 @@ index da3a2b0..dad1cef 100644 @echo 'Building file: $<' @echo 'Invoking: GCC C++ Compiler' - $(CC) -I${BAMTOOLS}/include -I${BAMTOOLS}/include/shared -I${SEQAN}/include -O3 -Wall -c -fmessage-length=0 -std=c++0x -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" -+ $(CC) -std=c++14 -I${PREFIX}/include/bamtools -I${PREFIX}/include/bamtools/shared -I${PREFIX}/include -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" ++ $(CXX) -std=c++14 -I${PREFIX}/include/bamtools -I${PREFIX}/include/bamtools/shared -I${PREFIX}/include -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" @echo 'Finished building: $<' @echo ' ' @@ -25,14 +25,14 @@ index da3a2b0..dad1cef 100644 @echo 'Building target: $@' @echo 'Invoking: GCC C++ Linker' - $(CC) -o $@ $(OBJS) -lboost_program_options -lboost_system -lboost_filesystem -lbamtools -L${BAMTOOLS}/lib -+ $(CC) -std=c++14 -o $@ $(OBJS) -lboost_program_options -lboost_system -lboost_filesystem -lbamtools -L${PREFIX}/lib ++ $(CXX) -std=c++14 -o $@ $(OBJS) -Wl,--copy-dt-needed-entries -lboost_program_options -lboost_system -lboost_filesystem -lbamtools -L${PREFIX}/lib @echo 'Finished building target: $@' @echo ' ' -diff --git i/SoftSV_1.4.2/src/Deletions.cpp w/src/Deletions.cpp +diff --git i/SoftSV_1.4.2/src/Deletions.cpp w/SoftSV_1.4.2/src/Deletions.cpp index 8ea7345..d44297d 100644 --- i/SoftSV_1.4.2/src/Deletions.cpp -+++ w/src/Deletions.cpp ++++ w/SoftSV_1.4.2/src/Deletions.cpp @@ -20,6 +20,8 @@ * @date 2015/09/09 */ @@ -69,10 +69,10 @@ index 8ea7345..d44297d 100644 std::stringstream output, bpSeq; -diff --git i/SoftSV_1.4.2/src/Inversions.cpp w/src/Inversions.cpp +diff --git i/SoftSV_1.4.2/src/Inversions.cpp w/SoftSV_1.4.2/src/Inversions.cpp index 207a774..ff4f8d9 100644 --- i/SoftSV_1.4.2/src/Inversions.cpp -+++ w/src/Inversions.cpp ++++ w/SoftSV_1.4.2/src/Inversions.cpp @@ -20,6 +20,8 @@ * @date 2015/09/09 */ @@ -109,10 +109,10 @@ index 207a774..ff4f8d9 100644 // Outpu format: // Chr Start End Support(PE) Support(SC) Upstream-breakpoint-sequence Downstream-breakpoint-sequence -diff --git i/SoftSV_1.4.2/src/Misc.cpp w/src/Misc.cpp +diff --git i/SoftSV_1.4.2/src/Misc.cpp w/SoftSV_1.4.2/src/Misc.cpp index bd10001..e0b460a 100644 --- i/SoftSV_1.4.2/src/Misc.cpp -+++ w/src/Misc.cpp ++++ w/SoftSV_1.4.2/src/Misc.cpp @@ -32,6 +32,8 @@ // Misc. basics @@ -122,10 +122,10 @@ index bd10001..e0b460a 100644 /** * @brief Returns the total length of small deletions within the CIGAR string of an alignment. -diff --git i/SoftSV_1.4.2/src/Tandems.cpp w/src/Tandems.cpp +diff --git i/SoftSV_1.4.2/src/Tandems.cpp w/SoftSV_1.4.2/src/Tandems.cpp index e6546af..7af0834 100644 --- i/SoftSV_1.4.2/src/Tandems.cpp -+++ w/src/Tandems.cpp ++++ w/SoftSV_1.4.2/src/Tandems.cpp @@ -20,6 +20,8 @@ * @date 2015/09/09 */ From 279df8d28bfd1bb3929007041c2329d083f6429d Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Fri, 13 Dec 2024 23:39:09 +0200 Subject: [PATCH 09/11] Fix the binary name and add test Signed-off-by: Martin Tzvetanov Grigorov --- recipes/softsv/build.sh | 4 +--- recipes/softsv/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/recipes/softsv/build.sh b/recipes/softsv/build.sh index 217a7aa6ed8cb..167528df7b1d7 100644 --- a/recipes/softsv/build.sh +++ b/recipes/softsv/build.sh @@ -4,7 +4,5 @@ set -xe CXX="${CXX} -std=c++14" make -j"${CPU_COUNT}" -ls -la - mkdir -p ${PREFIX}/bin -install -m 755 softsv ${PREFIX}/bin +install -m 755 SoftSV ${PREFIX}/bin diff --git a/recipes/softsv/meta.yaml b/recipes/softsv/meta.yaml index 3877c90cbd01d..9f10949f531d4 100644 --- a/recipes/softsv/meta.yaml +++ b/recipes/softsv/meta.yaml @@ -27,7 +27,7 @@ requirements: test: commands: - - ls -la # temporary + - SoftSV --help | grep {{ version }} about: home: https://sourceforge.net/projects/softsv From 1996cbc9b81e2bffa62c138206225e6ec466a430 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Sat, 14 Dec 2024 00:02:31 +0200 Subject: [PATCH 10/11] Add boost as runtime dependency --- recipes/softsv/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/softsv/meta.yaml b/recipes/softsv/meta.yaml index 9f10949f531d4..1012db6d554de 100644 --- a/recipes/softsv/meta.yaml +++ b/recipes/softsv/meta.yaml @@ -24,6 +24,8 @@ requirements: - boost-cpp - bamtools - seqan ==2.1.1 + run: + - boost-cpp test: commands: From 4758b9457e4e5538faae4302053d9189db9f2ef1 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Sat, 14 Dec 2024 00:44:54 +0200 Subject: [PATCH 11/11] =?UTF-8?q?Don=E2=80=99t=20build=20for=20OSX?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- recipes/softsv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/softsv/meta.yaml b/recipes/softsv/meta.yaml index 1012db6d554de..98bdc1ac350a7 100644 --- a/recipes/softsv/meta.yaml +++ b/recipes/softsv/meta.yaml @@ -7,6 +7,7 @@ package: build: number: 0 + skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -41,5 +42,4 @@ about: extra: additional-platforms: - - linux-aarch64 - - osx-arm64 \ No newline at end of file + - linux-aarch64 \ No newline at end of file