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Bioconductor package: an R wrapper for Bowtie2 and AdapterRemoval

Home Page: https://www.bioconductor.org/packages/release/bioc/html/Rbowtie2.html

R 1.27% C++ 94.53% Makefile 0.60% C 1.32% Perl 1.75% Python 0.27% CMake 0.26%

bioconductor bowtie2 r adapter

rbowtie2's Introduction

Rbowtie2

Bioconductor package: an R wrapper for Bowtie2 and AdapterRemoval

The Rbowtie2 package provides an R interface to the bowtie2 short read aligner by Langmead et al. (2009), and the AdapterRemoval package by Schubert, Lindgreen, and Orlando (2016). The Rbowtie2 package allows users to remove adapter sequences from reads, build bowtie2 indexes (.bt2 or .bt2l), and to create bowtie2 alignment files (.sam or .bam).

Additional Installation Instructions

The package interfaces with the bowtie2 and bowtie2-build wrapper scripts provided in the bowtie2 v2.4.4 source code. The bowtie2 wrapper script is a Perl script and the bowtie2-build wrapper script is a Python script. Most versions of MacOS and Linux distributions come with a version of Perl and Python pre-installed. On Windows, both Perl and Python do not come pre-installed and they must be downloaded and installed manually. If either Perl or Python are not installed on your system follow the links below to download and install them.

Python: https://www.python.org/downloads/

Perl: https://www.perl.org/get.html

The package also uses samtools to create bam files if it is present on the system. The reason for this is explained under the Bam File Creation heading. However, samtools is completely optional and the package can be used without it. To download samtools follow the link below.

samtools: http://www.htslib.org/download/

Bam File Creation

The Rbowtie2 package attempts to use samtools to create the bam file if present on the system. This method of creating the bam file avoids the need to create an intermediate sam file which might be infeasable depending on the size of the file and the available memory on the system. If samtoolsis not found on the system, the package attempts to create the bam file via Rsamtools which requires that an intermediate sam file be created prior to the bam file being created.

Bowtie2 Source Package Information

The Rbowtie2 package uses the bowtie2 v2.4.4 source code which was obtained from https://sourceforge.net/projects/bowtie-bio/. The folders doc, example, scripts, and some non-code files were deleted to reduce the package size.

rbowtie2's People

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rvarki mehdimerbah jsun martin-g

rbowtie2's Issues

Build failure on Linux ARM64

Hi,

We are working on adding support for Linux ARM64 for Bioconductor and we faced the following build problem:

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rbowtie2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Rbowtie2’ ...
** using staged installation
** libs
mkdir -p ../inst
(cd	adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c adapterset.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c alignment.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c argparse.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c debug.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c demultiplex.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq_enc.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq_io.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c linereader.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c linereader_joined.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_adapter_id.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_adapter_rm.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_demultiplex.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c scheduler.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c strutils.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c threads.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c timer.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c trimmed_reads.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c userconfig.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG   -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o
mv AdapterRemoval ../../inst/
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
(cd	adapterremoval && (make clean_o -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
rm -f *.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
(cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
g++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	-Ithird_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
g++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	-Ithird_party \
	-o bowtie2-build-l bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
g++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	-Ithird_party \
	-o bowtie2-align-s bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	 -lpthread -lz
In file included from aligner_sw.h:73,
                 from bt2_search.cpp:54:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_sw.cpp:25:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
                 from aligner_bt.h:31,
                 from aligner_bt.cpp:20:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
                 from sse_util.cpp:20:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
                 from aligner_swsse.h:28,
                 from aligner_swsse.cpp:22:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_loc_i16.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_ee_i16.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_loc_u8.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_ee_u8.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [Makefile:339: bowtie2-align-s] Error 1
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
make: *** [Makefile:12: all] Error 2
ERROR: compilation failed for package ‘Rbowtie2’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Rbowtie2’

bowtie2 uses Git Submodules to setup simde for non-x86_64 support: https://github.com/BenLangmead/bowtie2/blob/master/.gitmodules

Would you be interested in updating the packaging and building of the C++ code ?
I'd be glad to provide a Pull Request! I may just need a little guidance!

Thank you!

`Rbowtie2::bowtie2_samtools`: print to console during processing

Hi there, thanks for the great tool!

I'm incorporating Rbowtie2::bowtie2_samtools into my epigenomics pipeline, and I noticed the messages while running it:

arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only

This means that for non-Windows user, they won't see any of the bowtie2 output until everything is done processing (which can be a very long time). This make is difficult for users to assess whether the program is working or there has been some error and it's just hanging there.

Looked into the internal code and found that this is because .callBinary is using system(..., internal=TRUE).

I'm wondering if there's a way to both capture the output and print it to the user during processing. For instance, perhaps you could take advantage of the fact that bowtie2 is running in the command line and pipe its output to a text file. Here's an example of how we've done this in the past:

bowtie2 \
--local \ 
--very-sensitive \
--no-mixed \
--no-discordant \
--phred33 \
-I 10 \
-X 700 \
-p ${cores} \
-x ${ref} \
-1 ${datadir}/data_trimmed/${sample_name}_val_1.fq.gz \
-2 ${datadir}/data_trimmed/${sample_name}_val_2.fq.gz \
-S ${outdir}/${sample_name}_trimmed_bowtie2.sam &> ${outdir}/bowtie2_summary/${sample_name}_trimmed_bowtie2.txt

The CRAN package sys may or may not be helpful here too.

installation in MacOS

Hi!

everytime that I try to install Rhisat2, they ask me about accepting c/c++; when I write no... installation is terminated but when I write "Yes"... al theses errors appears.

How can I proceed in this situation. I am using MacOS apple silicon M1

kind regards

bowtie2_samtools

Hi,

First of all thanks for developing this package (hope to use it soon!). I have been trying to familiarize myself with the package, and while trying to run the 'introduction' code from the bioconductor page, the code stops at the 'bowtie2_samtools' function which seems to be missing. While it may be embedded and used within the 'bowtie2' function it cannot be called directly.

Thanks in advance,
Micah

update AdapterRemoval version

Hi, the Rbowtie2 use an old version for AdapterRemoval software. How to update AdapterRemoval version to the latest v2.2.3? Thanks!

Installation on Mac M1 MacOS Monterey

Hi!
I am trying to install Rbowtie2 using RSudio on my mac M1 (MacOS Monterey).
I could install bowtie2 from the sources provided on Github, but all my attemps to install the wrapper Rbowtie2 failed.
I am enclosing the console info below.
Do you have anyclue about how to solve this issue?
Thanks!

BiocManager::install('Rbowtie2')
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23)
Installing package(s) 'Rbowtie2'
Package which is only available in source form, and may need compilation of C/C++/Fortran:
‘Rbowtie2’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘Rbowtie2’

trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Rbowtie2_2.4.0.tar.gz'
Content type 'application/x-gzip' length 1227822 bytes (1.2 MB)

downloaded 1.2 MB

Loading custom .Rprofile* installing source package ‘Rbowtie2’ ...
** using staged installation
** libs
** arch -
mkdir -p ../inst
(cd adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile))
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c adapterset.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c alignment.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c argparse.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c debug.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c demultiplex.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_enc.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_io.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader_joined.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_id.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_rm.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_demultiplex.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c scheduler.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c strutils.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c threads.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c timer.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c trimmed_reads.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c userconfig.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o
mv AdapterRemoval ../../inst/
(cd adapterremoval && (make clean_o -f Makefile))
rm -f *.o
(cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile))
g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS=""-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1
-fno-strict-aliasing -DBOWTIE2_VERSION=""cat BOWTIE2_VERSION"" -DBUILD_HOST=""${HOSTNAME:-hostname}"" -DBUILD_TIME=""date -u"" -DCOMPILER_VERSION=""g++ -v 2>&1 | tail -1"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall
-Ithird_party
-o bowtie2-build-s bt2_build.cpp
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp
-lpthread -lz
g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS=""-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1
-fno-strict-aliasing -DBOWTIE2_VERSION=""cat BOWTIE2_VERSION"" -DBUILD_HOST=""${HOSTNAME:-hostname}"" -DBUILD_TIME=""date -u"" -DCOMPILER_VERSION=""g++ -v 2>&1 | tail -1"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall
-Ithird_party
-o bowtie2-build-l bt2_build.cpp
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp
-lpthread -lz
g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS=""-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1
-fno-strict-aliasing -DBOWTIE2_VERSION=""cat BOWTIE2_VERSION"" -DBUILD_HOST=""${HOSTNAME:-hostname}"" -DBUILD_TIME=""date -u"" -DCOMPILER_VERSION=""g++ -v 2>&1 | tail -1"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall
-Ithird_party
-o bowtie2-align-s bt2_search.cpp
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp
-lpthread -lz
In file included from aligner_sw.h:73,
from bt2_search.cpp:54:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
from aligner_sw.cpp:25:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
from aligner_sw_driver.h:81,
from aligner_sw_driver.cpp:47:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
from aligner_bt.h:31,
from aligner_bt.cpp:20:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
from sse_util.cpp:20:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
from aligner_swsse.h:28,
from aligner_swsse.cpp:22:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
from aligner_swsse_loc_i16.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
from aligner_swsse_ee_i16.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
from aligner_swsse_loc_u8.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
from aligner_swsse_ee_u8.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
31 | #include "simde/x86/sse2.h"
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [bowtie2-align-s] Error 1
make: *** [all] Error 2
ERROR: compilation failed for package ‘Rbowtie2’

removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rbowtie2’

The downloaded source packages are in
‘/private/var/folders/dn/q298x85j3j98njd17qkwzpc40000gr/T/RtmpD6HCPS/downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘Rbowtie2’ had non-zero exit status

Support with gz compressed fastq format

Hi, thanks for supplying this great package in R. Can it support with compressed fastq format with .gz as input? Maybe this is useful to save disk. Thanks.