pjotrp
commented
4 years ago That is a generated file from the make file. Please look at the travis build script.
Closed moldach closed 4 years ago
pjotrp
commented
4 years ago That is a generated file from the make file. Please look at the travis build script.
moldach
commented
4 years ago That is a generated file from the make file. Please look at the travis build script.
Sorry I'm not sure I follow you? You're saying the makefile generates a travis build script when it errors that I should look at?
This is what I see in the sambamba directory:
[moldach@cedar5 sambamba]$ ll
total 226
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:05 bin
drwxr-x--- 6 moldach moldach 4096 Apr 30 08:03 BioD
drwxr-x--- 3 moldach moldach 4096 Apr 30 08:03 contrib
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 cram
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 deb
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 doc
-rw-r----- 1 moldach moldach 204 Apr 30 08:03 dub.json
drwxr-x--- 3 moldach moldach 4096 Apr 30 08:03 etc
-rwxr-x--- 1 moldach moldach 827 Apr 30 08:03 gen_ldc_version_info.py
drwxr-x--- 5 moldach moldach 4096 Apr 30 08:05 htslib
-rw-r----- 1 moldach moldach 899 Apr 30 08:03 INSTALL.md
-rw-r----- 1 moldach moldach 17992 Apr 30 08:03 LICENSE
drwxr-x--- 9 moldach moldach 4096 Apr 30 08:03 lz4
-rw-r----- 1 moldach moldach 3576 Apr 30 08:03 Makefile
-rw-r----- 1 moldach moldach 2143 Apr 30 08:03 Makefile.docker
-rw-r----- 1 moldach moldach 4349 Apr 30 08:03 Makefile.guix
-rw-r----- 1 moldach moldach 3366 Apr 30 08:03 Makefile.old
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 man
-rw-r----- 1 moldach moldach 3659 Apr 30 08:03 meson.build
-rw-r----- 1 moldach moldach 58 Apr 30 08:03 meson_options.txt
-rw-r----- 1 moldach moldach 13072 Apr 30 08:03 README.md
-rw-r----- 1 moldach moldach 4393 Apr 30 08:03 RELEASE-NOTES.md
-rwxr-x--- 1 moldach moldach 292 Apr 30 08:03 run_tests.sh
drwxr-x--- 3 moldach moldach 4096 Apr 30 08:03 sambamba
-rw-r----- 1 moldach moldach 2633 Apr 30 08:03 sambamba-ldmd-debug.rsp
-rw-r----- 1 moldach moldach 2940 Apr 30 08:03 sambamba-ldmd-release.rsp
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 scripts
drwxr-x--- 4 moldach moldach 4096 Apr 30 08:03 test
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 thirdparty
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:05 utils
-rw-r----- 1 moldach moldach 6 Apr 30 08:03 VERSION
This is the error from running make:
[moldach@cedar5 sambamba]$ module load python/3.7
[moldach@cedar5 sambamba]$ make
cd lz4/lib && gcc -O3 -c lz4.c lz4hc.c lz4frame.c xxhash.c && ar rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o
cd htslib && make -j8
make[1]: Entering directory '/home/moldach/bin/sambamba/htslib'
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o kstring.o kstring.c
echo '/* Empty config.h generated by Makefile */' > config.h
echo '#define HTS_VERSION "0.2.0-rc10-271-g2f3c3ea"' > version.h
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o kfunc.pico kfunc.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o knetfile.pico knetfile.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o kstring.pico kstring.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o bgzf.pico bgzf.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o faidx.pico faidx.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o hfile.pico hfile.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o hts.pico hts.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o md5.pico md5.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o regidx.pico regidx.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o sam.pico sam.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o tbx.pico tbx.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o vcf.pico vcf.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/files.pico cram/files.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/thread_pool.pico cram/thread_pool.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/vlen.pico cram/vlen.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -fpic -c -o cram/zfio.pico cram/zfio.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o bgzip.o bgzip.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o htsfile.o htsfile.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o tabix.o tabix.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o test/fieldarith.o test/fieldarith.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o test/hfile.o test/hfile.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o test/sam.o test/sam.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o test/test-regidx.o test/test-regidx.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o test/test_view.o test/test_view.c
test/sam.c: In function ‘faidx1’:
test/sam.c:169:5: warning: ‘faidx_fetch_nseq’ is deprecated: Please use faidx_nseq instead [-Wdeprecated-declarations]
n = faidx_fetch_nseq(fai);
^
In file included from test/sam.c:32:0:
./htslib/faidx.h:94:9: note: declared here
int faidx_fetch_nseq(const faidx_t *fai) HTS_DEPRECATED("Please use faidx_nseq instead");
^
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o faidx.o faidx.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o hfile.o hfile.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o hfile_net.o hfile_net.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o hts.o hts.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o md5.o md5.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o regidx.o regidx.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o sam.o sam.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o tbx.o tbx.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o vcf.o vcf.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/vlen.o cram/vlen.c
gcc -g -Wall -O2 -D_GNU_SOURCE -I. -c -o cram/zfio.o cram/zfio.c
gcc -shared -Wl,-soname,libhts.so.1 -pthread -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico -lz -lm
ln -sf libhts.so libhts.so.1
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
gcc -pthread -o bgzip bgzip.o libhts.a -lz
gcc -pthread -o htsfile htsfile.o libhts.a -lz
gcc -pthread -o tabix tabix.o libhts.a -lz
gcc -pthread -o test/fieldarith test/fieldarith.o libhts.a -lz
gcc -o test/hfile test/hfile.o libhts.a -lz
gcc -pthread -o test/sam test/sam.o libhts.a -lz
gcc -pthread -o test/test-regidx test/test-regidx.o libhts.a -lz
gcc -pthread -o test/test_view test/test_view.o libhts.a -lz
gcc -pthread -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz
gcc -pthread -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz
make[1]: Leaving directory '/home/moldach/bin/sambamba/htslib'
mkdir -p bin/
compile single object...
ldc2 -singleobj -wi -I. -IBioD -g -J. -O3 -release -enable-inlining -boundscheck=off -L-lz -c -of=bin/sambamba-0.7.1.o utils/ldc_version_info_.d utils/lz4.d utils/strip_bcf_header.d BioD/contrib/undead/cstream.d BioD/contrib/undead/doformat.d BioD/contrib/undead/internal/file.d BioD/contrib/undead/stream.d BioD/contrib/undead/utf.d utils/version_.d BioD/bio/core/base.d BioD/bio/core/bgzf/block.d BioD/bio/core/bgzf/chunk.d BioD/bio/core/bgzf/compress.d BioD/bio/core/bgzf/constants.d BioD/bio/core/bgzf/inputstream.d BioD/bio/core/bgzf/outputstream.d BioD/bio/core/bgzf/virtualoffset.d BioD/bio/core/call.d BioD/bio/core/decompress.d BioD/bio/core/genotype.d BioD/bio/core/kmer.d BioD/bio/core/region.d BioD/bio/core/sequence.d BioD/bio/core/tinymap.d BioD/bio/core/utils/algo.d BioD/bio/core/utils/bylinefast.d BioD/bio/core/utils/exception.d BioD/bio/core/utils/format.d BioD/bio/core/utils/memoize.d BioD/bio/core/utils/outbuffer.d BioD/bio/core/utils/range.d BioD/bio/core/utils/roundbuf.d BioD/bio/core/utils/stream.d BioD/bio/core/utils/switchendianness.d BioD/bio/core/utils/tmpfile.d BioD/bio/core/utils/zlib.d BioD/bio/std/experimental/hts/bam/header.d BioD/bio/std/experimental/hts/bam/reader.d BioD/bio/std/experimental/hts/bam/writer.d BioD/bio/std/experimental/hts/bgzf.d BioD/bio/std/experimental/hts/bgzf_writer.d BioD/bio/std/experimental/hts/constants.d BioD/bio/std/experimental/hts/hashing.d BioD/bio/std/experimental/hts/logger.d BioD/bio/std/experimental/hts/pileup.d BioD/bio/std/experimental/hts/reads.d BioD/bio/std/experimental/hts/unpack.d BioD/bio/std/file/fai.d BioD/bio/std/file/fasta.d BioD/bio/std/file/fastq.d BioD/bio/std/genotype/maf.d BioD/bio/std/genotype/snp.d BioD/bio/std/hts/bam/abstractreader.d BioD/bio/std/hts/bam/bai/bin.d BioD/bio/std/hts/bam/bai/indexing.d BioD/bio/std/hts/bam/baifile.d BioD/bio/std/hts/bam/baseinfo.d BioD/bio/std/hts/bam/cigar.d BioD/bio/std/hts/bam/constants.d BioD/bio/std/hts/bam/md/core.d BioD/bio/std/hts/bam/md/operation.d BioD/bio/std/hts/bam/md/parse.d BioD/bio/std/hts/bam/md/reconstruct.d BioD/bio/std/hts/bam/multireader.d BioD/bio/std/hts/bam/pileup.d BioD/bio/std/hts/bam/randomaccessmanager.d BioD/bio/std/hts/bam/read.d BioD/bio/std/hts/bam/reader.d BioD/bio/std/hts/bam/readrange.d BioD/bio/std/hts/bam/reference.d BioD/bio/std/hts/bam/referenceinfo.d BioD/bio/std/hts/bam/region.d BioD/bio/std/hts/bam/splitter.d BioD/bio/std/hts/bam/tagvalue.d BioD/bio/std/hts/bam/validation/alignment.d BioD/bio/std/hts/bam/validation/samheader.d BioD/bio/std/hts/bam/writer.d BioD/bio/std/hts/iontorrent/flowcall.d BioD/bio/std/hts/iontorrent/flowindex.d BioD/bio/std/hts/sam/header.d BioD/bio/std/hts/sam/reader.d BioD/bio/std/hts/sam/utils/fastrecordparser.d BioD/bio/std/hts/sam/utils/recordparser.d BioD/bio/std/hts/snpcallers/maq.d BioD/bio/std/hts/snpcallers/simple.d BioD/bio/std/hts/thirdparty/msgpack.d BioD/bio/std/hts/utils/array.d BioD/bio/std/hts/utils/graph.d BioD/bio/std/hts/utils/samheadermerger.d BioD/bio/std/hts/utils/value.d BioD/bio/std/maf/block.d BioD/bio/std/maf/parser.d BioD/bio/std/maf/reader.d BioD/bio/std/range/splitter.d BioD/bio/std/sff/constants.d BioD/bio/std/sff/index.d BioD/bio/std/sff/read.d BioD/bio/std/sff/reader.d BioD/bio/std/sff/readrange.d BioD/bio/std/sff/utils/roundup.d BioD/bio/std/sff/writer.d cram/exception.d cram/htslib.d cram/reader.d cram/reference.d cram/slicereader.d cram/wrappers.d cram/writer.d sambamba/depth.d sambamba/fixbins.d sambamba/flagstat.d sambamba/index.d sambamba/main.d sambamba/markdup.d sambamba/markdup2.d sambamba/merge.d sambamba/pileup.d sambamba/slice.d sambamba/sort.d sambamba/subsample.d sambamba/utils/common/bed.d sambamba/utils/common/file.d sambamba/utils/common/filtering.d sambamba/utils/common/intervaltree.d sambamba/utils/common/ldc_gc_workaround.d sambamba/utils/common/overwrite.d sambamba/utils/common/pratt_parser.d sambamba/utils/common/progressbar.d sambamba/utils/common/queryparser.d sambamba/utils/common/readstorage.d sambamba/utils/common/tmpdir.d sambamba/utils/view/alignmentrangeprocessor.d sambamba/utils/view/headerserializer.d sambamba/validate.d sambamba/view.d thirdparty/mergesort.d thirdparty/unstablesort.d
sambamba/main.d(45): Error: module ldc_version_info_ from file utils/ldc_version_info_.d must be imported with 'import ldc_version_info_;'
make: *** [Makefile:93: singleobj] Error 1Yes what is this?
Can you please explain what I need to do with the link you provided? I'm not familiar with Travis Continous Integration other then it's a tool to help developers (you)
pjotrp
commented
4 years ago Look at the build log. That is what you should be doing.
pjotrp
commented
4 years ago Why not install the binary downloads or bioconda?
moldach
commented
4 years ago Look at the build log. That is what you should be doing.
This is what I see in the sambamba directory:
[moldach@cedar5 sambamba]$ ll
total 226
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:05 bin
drwxr-x--- 6 moldach moldach 4096 Apr 30 08:03 BioD
drwxr-x--- 3 moldach moldach 4096 Apr 30 08:03 contrib
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 cram
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 deb
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 doc
-rw-r----- 1 moldach moldach 204 Apr 30 08:03 dub.json
drwxr-x--- 3 moldach moldach 4096 Apr 30 08:03 etc
-rwxr-x--- 1 moldach moldach 827 Apr 30 08:03 gen_ldc_version_info.py
drwxr-x--- 5 moldach moldach 4096 Apr 30 08:05 htslib
-rw-r----- 1 moldach moldach 899 Apr 30 08:03 INSTALL.md
-rw-r----- 1 moldach moldach 17992 Apr 30 08:03 LICENSE
drwxr-x--- 9 moldach moldach 4096 Apr 30 08:03 lz4
-rw-r----- 1 moldach moldach 3576 Apr 30 08:03 Makefile
-rw-r----- 1 moldach moldach 2143 Apr 30 08:03 Makefile.docker
-rw-r----- 1 moldach moldach 4349 Apr 30 08:03 Makefile.guix
-rw-r----- 1 moldach moldach 3366 Apr 30 08:03 Makefile.old
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 man
-rw-r----- 1 moldach moldach 3659 Apr 30 08:03 meson.build
-rw-r----- 1 moldach moldach 58 Apr 30 08:03 meson_options.txt
-rw-r----- 1 moldach moldach 13072 Apr 30 08:03 README.md
-rw-r----- 1 moldach moldach 4393 Apr 30 08:03 RELEASE-NOTES.md
-rwxr-x--- 1 moldach moldach 292 Apr 30 08:03 run_tests.sh
drwxr-x--- 3 moldach moldach 4096 Apr 30 08:03 sambamba
-rw-r----- 1 moldach moldach 2633 Apr 30 08:03 sambamba-ldmd-debug.rsp
-rw-r----- 1 moldach moldach 2940 Apr 30 08:03 sambamba-ldmd-release.rsp
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 scripts
drwxr-x--- 4 moldach moldach 4096 Apr 30 08:03 test
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:03 thirdparty
drwxr-x--- 2 moldach moldach 4096 Apr 30 08:05 utils
-rw-r----- 1 moldach moldach 6 Apr 30 08:03 VERSIONWhere is the Travis build log? I see meson.build but this doesn't look like a log file
moldach
commented
4 years ago Why not install the binary downloads or bioconda?
We work on a shared academic HPC and ComputeCanada admins forbid us from using conda.
I run into issue for the binary install as well.
For those not in the mood to learn/install new package managers, there are Github source and binary releases. Simply download the tarball, unpack it and run it according to the accompanying release notes.
(.venv) [moldach@cedar5 sambamba-0.7.1]$ make
make: *** No rule to make target 'lz4/lib/lz4.c', needed by 'lz4/lib/liblz4.a'. Stop.According to INSTALL.md one of the dependencies liblz4 is not installed. According to their documentation:
make
make install # this command may require root permissionsSo it fails at this point because of the lack of root permissions on HPCs. I will have to talk to an admin I suppose.
pjotrp
commented
4 years ago ComputeCanada runs Nix packages - they have sambamba.
pjotrp
commented
4 years ago Also the binary download of sambamba has all dependencies included. Download and run.
I'm getting an error trying to install
Sambambaon LinuxInstalling LDC
Sambama
Looks like the error is: