Skip to content

Apply patch required to build necat in bioconda #25

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
natir wants to merge 1 commit into
base: master
Choose a base branch
from
+48 −48
Open

Apply patch required to build necat in bioconda #25

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion src/asm_pm/asmpm.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := asmpm.c find_mem.c km_chain.c blockwise_edlib.c daligner.c align.c h
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/consensus/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c read_id_pool.c cns_options.c error_estimate.c overlaps_pool.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++ -lm
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/ctg_cns/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ SOURCES := main.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/ctg_cns/pm4_main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := pm4_main.c pm4.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/ctgpm/ctgpm.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := ctgpm_main.c ctgpm.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++ -lm
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/ctgpm/fix_can_info.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := fix_can_info.c split_ctgs.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/ctgpm/split_ctgs.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := split_ctgs.c split_ctgs_main.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/extract_sequences/extract_sequences.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := extract_sequences.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
4 changes: 2 additions & 2 deletions src/fsa/assemble.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ TARGET := fsa_assemble
SOURCES := ./prog/fsa_assemble.cpp assembly.cpp graph.cpp string_graph.cpp path_graph.cpp

SRC_INCDIRS := .
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 ${CXXFLAGS}

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lfsa
TGT_LDLIBS := -lfsa -lz -lpthread
TGT_PREREQS := libfsa.a

SUBMAKEFILES :=
4 changes: 2 additions & 2 deletions src/fsa/bridge.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ TARGET := fsa_ctg_bridge
SOURCES := ./prog/fsa_ctg_bridge.cpp contig_bridge.cpp contig_graph.cpp contig_link.cpp contig_link_store.cpp

SRC_INCDIRS := .
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 ${CXXFLAGS}

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lfsa
TGT_LDLIBS := -lfsa -lz -lpthread
TGT_PREREQS := libfsa.a

SUBMAKEFILES :=
4 changes: 2 additions & 2 deletions src/fsa/filter.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ TARGET := fsa_ol_filter
SOURCES := ./prog/fsa_ol_filter.cpp

SRC_INCDIRS := .
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 ${CXXFLAGS}

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lfsa
TGT_LDLIBS := -lfsa -lz -lpthread
TGT_PREREQS := libfsa.a

SUBMAKEFILES :=
6 changes: 3 additions & 3 deletions src/fsa/fsa.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ SOURCES := argument_parser.cpp logger.cpp overlap.cpp read_store.cpp sequence.c
utility.cpp file_io.cpp seq_io.cpp overlap_store.cpp \
./simple_align.cpp overlap_filter.cpp overlap_stat.cpp overlap_trim.cpp

TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64
SRC_INCDIRS := .
TGT_CXXFLAGS := ${TGT_CXXFLAGS} -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 ${CXXFLAGS}
SRC_INCDIRS := . -I${PREFIX}/include

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
4 changes: 2 additions & 2 deletions src/fsa/rd_extract.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ TARGET := fsa_rd_extract
SOURCES := ./prog/fsa_rd_extract.cpp read_extract.cpp

SRC_INCDIRS := .
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 ${CXXFLAGS}

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lfsa
TGT_LDLIBS := -lfsa -lz
TGT_PREREQS := libfsa.a

SUBMAKEFILES :=
4 changes: 2 additions & 2 deletions src/fsa/rd_stat.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ TARGET := fsa_rd_stat
SOURCES := ./prog/fsa_rd_stat.cpp read_stat.cpp

SRC_INCDIRS := .
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 ${CXXFLAGS}

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lfsa
TGT_LDLIBS := -lfsa -lz
TGT_PREREQS := libfsa.a

SUBMAKEFILES :=
4 changes: 2 additions & 2 deletions src/fsa/rd_tools.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ TARGET := fsa_rd_tools
SOURCES := ./prog/fsa_rd_tools.cpp read_tools.cpp

SRC_INCDIRS := .
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64
TGT_CXXFLAGS := -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 ${CXXFLAGS}

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lfsa
TGT_LDLIBS := -lfsa -lz
TGT_PREREQS := libfsa.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/makedb/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/pairwise_mapping/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/partition_candidates/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c pcan_options.c pcan.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/partition_m4/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c pm4_options.c pm4.c pm4_aux.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/pm_one_volume/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c pm_worker.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/preprocess_raw_reads/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c truncate_end_spaces.cpp
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/reference_mapping/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c rm_worker.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/reference_mapping/rm_one_vol_main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := rm_one_vol_main.c rm_worker.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/renumber_sequences/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/reorder_cns_reads/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/sequence_length_stats/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/split_long_reads/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/test/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := main.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases/extract_trimmed_reads.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,8 @@ SOURCES := extract_trimmed_reads.c largest_cover_range.c range_list.c detect_ch

SRC_INCDIRS := .

TGT_LDLIBS := -lontcns -lz -lpthread
TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases/largest_cover_range.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ SOURCES := pm4_aux.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases/order_results.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := order_results.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases/pm4.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := pm4_aux.c pm4_main.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases/trim_bases.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := trim_bases.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases_accurate/largest_cover_range.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ SOURCES := pm4_aux.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++ -lm
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases_accurate/pm4.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := pm4_aux.c pm4_main.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases_accurate/trim_bases.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := trim_bases.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases_accurate0/largest_cover_range.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ SOURCES := pm4_aux.c \
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++ -lm
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases_accurate0/pm4.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := pm4_aux.c pm4_main.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lpthread
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion src/trim_bases_accurate0/trim_bases.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SOURCES := trim_bases.c
SRC_INCDIRS := .

TGT_LDFLAGS := -L${TARGET_DIR}
TGT_LDLIBS := -lontcns
TGT_LDLIBS := -lontcns -lz
TGT_PREREQS := libontcns.a

SUBMAKEFILES :=
2 changes: 1 addition & 1 deletion tool/main.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ ${TARGET_DIR}/pigz: ${TARGET_DIR}/../pigz-2.4/pigz

${TARGET_DIR}/../pigz-2.4/pigz: ../tool/pigz-2.4.tar.gz
tar -xzf ../tool/pigz-2.4.tar.gz -C ${TARGET_DIR}/.. || exit 255
cd ${TARGET_DIR}/../pigz-2.4 && make
cd ${TARGET_DIR}/../pigz-2.4 && make CC=${CC} LDFLAGS="${LDFLAGS}"

clean:
rm -f ${TARGET_DIR}/pigz
Expand Down