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Update mothur to 1.48.3 (#47909)
* Update mothur to 1.48.1 * add run_exports * Update mothur to 1.48.2 * Update meta.yaml * Update build.sh * Update mothur to 1.48.3 * Update build.sh * clean up recipe * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * clean up recipe * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * edit patches * Update meta.yaml * Update build.sh * edit patch * Update build.sh * Update build.sh * edit patch * Update build.sh * clean up recipe * clean up recipe * edit build.sh * add osx patch * Update 0003-uchime_makefile.patch --------- Co-authored-by: Joshua Zhuang <[email protected]> Co-authored-by: mencian <[email protected]>
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‎recipes/mothur/makefile.patch renamed to ‎recipes/mothur/0001-Makefile.patch

Lines changed: 37 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,15 @@
1-
--- Makefile.org 2021-07-16 10:32:49.601483436 +0000
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+++ Makefile 2021-07-19 14:38:06.132941601 +0000
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diff --git a/Makefile b/Makefile
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index 8eb055f..d20d02c 100644
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--- a/Makefile
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+++ b/Makefile
35
@@ -20,21 +20,21 @@
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# GSL_INCLUDE_DIR - location of GSL include files
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# MOTHUR_FILES - The MOTHUR_FILES parameter is optional, but allows you to set a default location for mothur to look for input files it can't find. This is often used for reference files you want to store in one location separate from your data.
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-INSTALL_DIR ?= "\"Enter_your_mothur_install_path_here\""
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+INSTALL_DIR ?= "$(PREFIX)/bin"
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10-
-OPTIMIZE ?= yes
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+OPTIMIZE ?= no
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OPTIMIZE ?= yes
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USEREADLINE ?= yes
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-USEBOOST ?= no
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-USEHDF5 ?= no
@@ -32,4 +33,35 @@
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+GSL_INCLUDE_DIR ?= "$(PREFIX)/include/gsl"
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MOTHUR_FILES="\"Enter_your_default_path_here\""
3435
MOTHUR_TOOLS="\"Enter_your_mothur_tools_path_here\""
35-
VERSION = "\"1.45.2\""
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VERSION = "\"1.48.3\""
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@@ -50,8 +50,8 @@ ifeq ($(strip $(OPTIMIZE)),yes)
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CXXFLAGS += -O3
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endif
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-CXXFLAGS += -std=c++11 -pthread -DVERSION=${VERSION} -DRELEASE_DATE=${RELEASE_DATE}
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-LDFLAGS += -std=c++11 -pthread
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+CXXFLAGS += -I$(PREFIX)/include -std=c++14 -pthread -DVERSION=${VERSION} -DRELEASE_DATE=${RELEASE_DATE}
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+LDFLAGS += -L$(PREFIX)/lib -std=c++14 -pthread
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ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
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else
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@@ -109,8 +109,8 @@ endif
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subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/))))
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subDirIncludes = $(patsubst %, -I %, $(subdirs))
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subDirLinking = $(patsubst %, -L%, $(subdirs))
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- CXXFLAGS += -I. $(subDirIncludes)
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- LDFLAGS += $(subDirLinking)
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+ CXXFLAGS += -I. -Isource $(subDirIncludes)
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+ LDFLAGS += -Lsource $(subDirLinking)
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#
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@@ -132,7 +132,7 @@ install : mothur
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ifeq ($(strip $(INSTALL_DIR)),"\"Enter_your_mothur_install_path_here\"")
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else
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mkdir -p ${INSTALL_DIR}
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- mv mothur ${INSTALL_DIR}/mothur
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+ install -v -m 0755 mothur ${INSTALL_DIR}
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endif
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‎recipes/mothur/0002-Makefile-osx.patch

Lines changed: 24 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
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diff --git a/Makefile b/Makefile
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index d20d02c..a805ca0 100644
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--- a/Makefile
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+++ b/Makefile
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@@ -109,8 +109,8 @@ endif
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subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/))))
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subDirIncludes = $(patsubst %, -I %, $(subdirs))
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subDirLinking = $(patsubst %, -L%, $(subdirs))
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- CXXFLAGS += -I. -Isource $(subDirIncludes)
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- LDFLAGS += -Lsource $(subDirLinking)
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+ CXXFLAGS += -I. -Isource/ $(subDirIncludes)
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+ LDFLAGS += -Lsource/ $(subDirLinking)
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14+
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#
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@@ -118,6 +118,8 @@ endif
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#
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OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
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OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
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+ OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard source/*.cpp))
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+ OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard source/*.c))
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OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
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OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
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‎recipes/mothur/0003-uchime_makefile.patch

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,27 @@
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diff --git a/source/uchime_src/makefile b/source/uchime_src/makefile
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index 428babe..615936e 100644
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--- a/source/uchime_src/makefile
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+++ b/source/uchime_src/makefile
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@@ -1,5 +1,5 @@
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-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
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-LDFLAGS = -g
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+CXXFLAGS = -std=c++14 -O3 -I$(PREFIX)/include -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
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+LDFLAGS = -L$(PREFIX)/lib -g
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#
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# Get the list of all .cpp files, rename to .o files
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@@ -14,7 +14,6 @@ uchime : $(OBJECTS)
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install : uchime
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-
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%.o : %.c %.h
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$(COMPILE.c) $(OUTPUT_OPTION) $<
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%.o : %.cpp %.h
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@@ -26,4 +25,4 @@ install : uchime
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clean :
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@rm -f $(OBJECTS)
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-
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\ No newline at end of file
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+

‎recipes/mothur/build.sh

Lines changed: 25 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,18 +1,32 @@
1-
### Dumping preset flags because they break the build process on linux
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# Linker flags
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unset LDFLAGS
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export LDFLAGS="-L${PREFIX}/lib"
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# Compiler flags
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unset CXXFLAGS
7-
export CXXFLAGS="-I${PREFIX}/include -I."
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#!/bin/bash
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3+
export CPLUS_INCLUDE_PATH="${PREFIX}/include"
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export LIBRARY_PATH="${PREFIX}/lib"
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export INCLUDES="-I${PREFIX}/include"
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export LIBPATH="-L${PREFIX}/lib"
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if [[ "$(uname -s)" == "Darwin" ]]; then
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export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib -headerpad_max_install_names"
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sed -i.bak 's/-std=c++14/-std=c++14 -stdlib=libc++/' Makefile
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sed -i.bak 's/-std=c++14/-std=c++14 -stdlib=libc++/' source/uchime_src/makefile
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else
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### Dumping preset flags because they break the build process on linux
14+
# Linker flags
15+
unset LDFLAGS
16+
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
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fi
18+
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sed -i.bak 's/OPTIMIZE ?= yes/OPTIMIZE ?= no/' Makefile
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rm -rf *.bak
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### Compiling mothur
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make clean
12-
make -j 4
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25+
make CXX="${CXX}" -j"${CPU_COUNT}"
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1327
make install
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cp -a uchime ${PREFIX}/bin
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install -v -m 0755 uchime "${PREFIX}/bin"
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# Linking BLAST binaries to default location for mothur
17-
mkdir -pv "${PREFIX}"/bin/blast/bin/
18-
ln -s "${PREFIX}"/bin/{blastall,formatdb,megablast} "${PREFIX}"/bin/blast/bin/
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mkdir -pv "${PREFIX}/bin/blast/bin"
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ln -sf "${PREFIX}"/bin/{blastall,formatdb,megablast} "${PREFIX}/bin/blast/bin/"

‎recipes/mothur/build_failure.linux-64.yaml

Lines changed: 0 additions & 104 deletions
This file was deleted.

‎recipes/mothur/meta.yaml

Lines changed: 31 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,58 +1,70 @@
1-
{% set mothurVersion = "1.48.0" %}
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{% set mothurSha256 = "9494406abd8d14b821782ab9db811f045ded9424f28f01234ee6764d4e78941d" %}
1+
{% set name = "mothur" %}
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{% set mothurVersion = "1.48.3" %}
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{% set mothurSha256 = "70129ef4f7cae5840aece54a1f4097a5044b824c9e62b9fcc7460ad70d4de3c0" %}
34
{% set vsearchVersion = "2.15.2" %}
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56
package:
6-
name: mothur
7+
name: {{ name }}
78
version: {{ mothurVersion }}
89

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source:
1011
url: https://github.com/mothur/mothur/archive/refs/tags/v{{ mothurVersion }}.tar.gz
1112
sha256: {{ mothurSha256 }}
1213
patches:
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- makefile.patch
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- 0001-Makefile.patch
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- 0002-Makefile-osx.patch # [osx]
16+
- 0003-uchime_makefile.patch
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1518
build:
16-
number: 3
19+
number: 0
20+
run_exports:
21+
- {{ pin_subpackage('mothur', max_pin="x") }}
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1823
requirements:
1924
build:
20-
- make==4.2.1
25+
- make
2126
- {{ compiler('c') }}
2227
- {{ compiler('cxx') }}
2328
host:
24-
- blast-legacy
2529
- boost-cpp
2630
- gsl
2731
- hdf5
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- readline
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- sra-tools
30-
- vsearch ={{ vsearchVersion }}
33+
- sra-tools # [not arm64]
34+
- vsearch >=2.15.2
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#- vsearch ={{ vsearchVersion }} # [x86_64]
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#- vsearch >=2.28.1 # [aarch64 or arm64]
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- zlib
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- bzip2
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run:
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- blast-legacy
3440
- boost-cpp
3541
- gsl
3642
- hdf5
3743
- readline
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- sra-tools
39-
- vsearch ={{ vsearchVersion }}
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- zlib
44+
- sra-tools # [not arm64]
45+
- vsearch >=2.15.2
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#- vsearch ={{ vsearchVersion }} # [x86_64]
47+
#- vsearch >=2.28.1 # [aarch64 or arm64]
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4249
test:
4350
commands:
4451
- mothur "#help()"
4552
- uchime --version
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4754
about:
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home: http://www.mothur.org
49-
license: GPL-3.0
50-
license_family: GPL
51-
license_file: LICENSE.md
52-
summary: This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
53-
dev_url: https://github.com/mothur/mothur
55+
home: "https://www.mothur.org"
56+
license: "GPL-3.0-or-later"
57+
license_family: GPL3
58+
license_file: "LICENSE.md"
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summary: "This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community."
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dev_url: "https://github.com/mothur/mothur"
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doc_url: "https://mothur.org/wiki/mothur_manual"
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extra:
5664
identifiers:
5765
- doi:10.1128/AEM.01541-09
5866
- usegalaxy-eu:mothur_get_label
67+
- biotools:mothur
68+
additional-platforms:
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- linux-aarch64
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- osx-arm64

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