Add -Wl,--copy-dt-needed-entries for the linker

https://stackoverflow.com/a/55086637/497381 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
bioconda · Dec 13, 2024 · 664275a · 664275a
1 parent 2b5a1c2
commit 664275a
Showing 1 changed file with 207 additions and 13 deletions.
diff --git a/recipes/softsv/softsv.patch b/recipes/softsv/softsv.patch
@@ -1,7 +1,7 @@
-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
+diff --git i/makefile w/makefile
+index da3a2b0..0294964 100644
+--- i/makefile
++++ w/makefile
 @@ -2,7 +2,7 @@
 
  # You may need to modify the following paths:
@@ -25,13 +25,207 @@ 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 
++	$(CC) -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/src/Analysis.d w/src/Analysis.d
+index 8be3017..089db1c 100644
+--- i/src/Analysis.d
++++ w/src/Analysis.d
+@@ -1220,6 +1220,8 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/platform.h \
++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/platform/platform_gcc.h \
++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/platform/platform_nvcc.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_debug.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/debug_test_system.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/debug_helper.h \
+@@ -1308,9 +1310,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_tangle.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_view.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_device.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/simd.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/simd/simd_base.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/simd/simd_base_seqan_impl.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/misc/bit_twiddling_functors.h \
+@@ -1344,6 +1343,8 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence/string_set_owner.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence/string_set_segment.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel.h \
++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_critical_section.h \
++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_condition.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_tags.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_macros.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_atomic_primitives.h \
+@@ -1356,9 +1357,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_queue_suspendable.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_resource_pool.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_serializer.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/enumerable_thread_local.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/enumerable_thread_local_iterator.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_thread_pool.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_alphabet.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_alphabet_expansion.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_iterator.h \
+@@ -1372,7 +1370,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_shortcuts.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_cyclic_shape.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_position.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_padding.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_metafunctions.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/graph_align.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/score.h \
+@@ -1385,8 +1382,10 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_forwards.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_forwards.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_base.h \
++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_mutex.h \
++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_event.h \
++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_thread.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_sync.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_event_win.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_async.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_directory.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/file/file_page.h \
+@@ -1409,7 +1408,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_io.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_data.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_dyn.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_simple.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/fragment.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/graph_types.h \
+@@ -1479,7 +1477,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_config.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_traceback.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/matrix_base.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/aligned_sequence_concept.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_base.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_iterator_base.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_array.h \
+@@ -1492,11 +1489,11 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/alignment_algorithm_tags.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_profile.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_band.h \
++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_scout.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_linear.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_affine.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_dynamic.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_scout.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_trace_segment.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_traceback_adaptor.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_formula.h \
+@@ -1519,7 +1516,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_myers_hirschberg_impl.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_waterman_eggert_impl.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h \
+- /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_interface_wrapper.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_unbanded.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_banded.h \
+  /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_unbanded.h \
+@@ -2753,6 +2749,8 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/platform.h:
++/home/mgrigorov/miniconda3/envs/test123/include/seqan/platform/platform_gcc.h:
++/home/mgrigorov/miniconda3/envs/test123/include/seqan/platform/platform_nvcc.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_debug.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/debug_test_system.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/debug_helper.h:
+@@ -2841,9 +2839,6 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_tangle.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_view.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_device.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/simd.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/simd/simd_base.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/simd/simd_base_seqan_impl.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/misc/bit_twiddling_functors.h:
+@@ -2877,6 +2872,8 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence/string_set_owner.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence/string_set_segment.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel.h:
++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_critical_section.h:
++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_condition.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_tags.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_macros.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_atomic_primitives.h:
+@@ -2889,9 +2886,6 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_queue_suspendable.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_resource_pool.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_serializer.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/enumerable_thread_local.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/enumerable_thread_local_iterator.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_thread_pool.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_alphabet.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_alphabet_expansion.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_iterator.h:
+@@ -2905,7 +2899,6 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_shortcuts.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_cyclic_shape.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_position.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_padding.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_metafunctions.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/graph_align.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/score.h:
+@@ -2918,8 +2911,10 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_forwards.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_forwards.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_base.h:
++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_mutex.h:
++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_event.h:
++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_thread.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_sync.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_event_win.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_async.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_directory.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/file/file_page.h:
+@@ -2942,7 +2937,6 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_io.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_data.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_dyn.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_simple.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/fragment.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/graph_types.h:
+@@ -3012,7 +3006,6 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_config.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_traceback.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/matrix_base.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/align/aligned_sequence_concept.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_base.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_iterator_base.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_array.h:
+@@ -3025,11 +3018,11 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/alignment_algorithm_tags.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_profile.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_band.h:
++/home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_scout.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_linear.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_affine.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_dynamic.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_scout.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_trace_segment.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_traceback_adaptor.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_formula.h:
+@@ -3052,7 +3045,6 @@ src/Misc.cpp:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_myers_hirschberg_impl.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_waterman_eggert_impl.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:
+-/home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_interface_wrapper.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_unbanded.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_banded.h:
+ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_unbanded.h:
+diff --git i/src/Deletions.cpp w/src/Deletions.cpp
 index 8ea7345..d44297d 100644
---- i/SoftSV_1.4.2/src/Deletions.cpp
+--- i/src/Deletions.cpp
 +++ w/src/Deletions.cpp
 @@ -20,6 +20,8 @@
   * @date 2015/09/09
@@ -69,9 +263,9 @@ 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/src/Inversions.cpp w/src/Inversions.cpp
 index 207a774..ff4f8d9 100644
---- i/SoftSV_1.4.2/src/Inversions.cpp
+--- i/src/Inversions.cpp
 +++ w/src/Inversions.cpp
 @@ -20,6 +20,8 @@
   * @date 2015/09/09
@@ -109,9 +303,9 @@ 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/src/Misc.cpp w/src/Misc.cpp
 index bd10001..e0b460a 100644
---- i/SoftSV_1.4.2/src/Misc.cpp
+--- i/src/Misc.cpp
 +++ w/src/Misc.cpp
 @@ -32,6 +32,8 @@
 
@@ -122,9 +316,9 @@ 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/src/Tandems.cpp w/src/Tandems.cpp
 index e6546af..7af0834 100644
---- i/SoftSV_1.4.2/src/Tandems.cpp
+--- i/src/Tandems.cpp
 +++ w/src/Tandems.cpp
 @@ -20,6 +20,8 @@
   * @date 2015/09/09