No clear instruction on installation

[emmannaemeka]

Hello,

There seem to be no clear instruction on how to install this program. Can it be made simpler?

[adigenova]

HI, The simplest way is to download the Linux pre-compiled binaries from here:

https://github.com/adigenova/wengan/releases/download/0.1/wengan-v0.1-bin-Linux.tar.gz

there is demo repository with detailed instructions here:

https://github.com/adigenova/wengan_demo

best, Alex

[emmannaemeka]

Thanks

Followed this process

export WG=/home/emmanuel/wengan-v0.1-bin-Linux/wengan.pl

qsub wengan.qsub

Error

/home/emmanuel/wengan-v0.1-bin-Linux/bin/minia -in mucuna.minia_reads.41.txt -kmer-size 41 -abundance-min 2 -out mucuna.minia.41 -minimizer-size 10 -max-memory 5000 -nb-cores 1 2> mucuna.minia.41.err > mucuna.minia.41.log

make: *** [mucuna.minia.41.contigs.fa] Error 1

Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Feb 10, 2020 at 9:16 AM adigenova notifications@github.com wrote:

HI, The simplest way is to download the Linux pre-compiled binaries from here:

https://github.com/adigenova/wengan/releases/download/0.1/wengan-v0.1-bin-Linux.tar.gz

there is demo repository with detailed instructions here:

https://github.com/adigenova/wengan_demo

best, Alex

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/adigenova/wengan/issues/14?email_source=notifications&email_token=AHVLNZYNKCZ3Q47C6EXYT4TRCEENVA5CNFSM4KSERXO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELHTKCA#issuecomment-584004872, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ3AEXBKIWUG5LZ4Z63RCEENVANCNFSM4KSERXOQ .

[adigenova]

can you post the content of :

mucuna.minia.41.log and mucuna.minia.41.err

thanks

[emmannaemeka]

cat mucuna.minia.41.err

/home/emmanuel/wengan-v0.1-bin-Linux/bin/minia: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/emmanuel/wengan-v0.1-bin-Linux/bin/minia)

/home/emmanuel/wengan-v0.1-bin-Linux/bin/minia: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/emmanuel/wengan-v0.1-bin-Linux/bin/minia)

/home/emmanuel/wengan-v0.1-bin-Linux/bin/minia: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/emmanuel/wengan-v0.1-bin-Linux/bin/minia)

/home/emmanuel/wengan-v0.1-bin-Linux/bin/minia: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/emmanuel/wengan-v0.1-bin-Linux/bin/minia)

/home/emmanuel/wengan-v0.1-bin-Linux/bin/minia: /lib64/libstdc++.so.6: version `CXXABI_1.3.11' not found (required by /home/emmanuel/wengan-v0.1-bin-Linux/bin/minia)

mucuna.minia.41.log is empty

cat wengan.log

/home/emmanuel/wengan-v0.1-bin-Linux/bin/abyss-pe name=mucuna.abyss2 k=96 B=20G H=4 kc=3 v=-v np=1 lib="pe1" pe1="/mnt/data/emmanuel/wengan/MS01_Mucuna_R1_001._paired.fastq.gz /mnt/data/emmanuel/wengan/MS01_Mucuna_R2_001._paired.fastq.gz" contigs 2> mucuna.abyss2.err > mucuna.abyss2.log

make: *** [mucuna.abyss2-contigs.fa] Error 2

/home/emmanuel/wengan-v0.1-bin-Linux/bin/minia -in mucuna.minia_reads.41.txt -kmer-size 41 -abundance-min 2 -out mucuna.minia.41 -minimizer-size 10 -max-memory 5000 -nb-cores 1 2> mucuna.minia.41.err > mucuna.minia.41.log

make: *** [mucuna.minia.41.contigs.fa] Error 1

Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Feb 10, 2020 at 10:31 AM Emmanuel Nnadi eennadi@gmail.com wrote:

Thanks

Followed this process

export WG=/home/emmanuel/wengan-v0.1-bin-Linux/wengan.pl

qsub wengan.qsub

Error

/home/emmanuel/wengan-v0.1-bin-Linux/bin/minia -in mucuna.minia_reads.41.txt -kmer-size 41 -abundance-min 2 -out mucuna.minia.41 -minimizer-size 10 -max-memory 5000 -nb-cores 1 2> mucuna.minia.41.err > mucuna.minia.41.log

make: *** [mucuna.minia.41.contigs.fa] Error 1

Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Feb 10, 2020 at 9:16 AM adigenova notifications@github.com wrote:

HI, The simplest way is to download the Linux pre-compiled binaries from here:

https://github.com/adigenova/wengan/releases/download/0.1/wengan-v0.1-bin-Linux.tar.gz

there is demo repository with detailed instructions here:

https://github.com/adigenova/wengan_demo

best, Alex

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/adigenova/wengan/issues/14?email_source=notifications&email_token=AHVLNZYNKCZ3Q47C6EXYT4TRCEENVA5CNFSM4KSERXO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELHTKCA#issuecomment-584004872, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ3AEXBKIWUG5LZ4Z63RCEENVANCNFSM4KSERXOQ .

[adigenova]

The problem is that the pre-compiled binaries not found the required GLIB version (`GLIBCXX_3.4.21' not found). So, you have to re-compile from the sources.

the commands should be like this:

fetch Wengan and its components

git clone --recursive https://github.com/adigenova/wengan.git wengan

for each component, there are specific instructions.

I recommend to start building the WenganM pipeline, it requires the compilation of Minia3, fastmin-sg, intervalmiss, liger and seqtk.

To compile fastmin-sg, intervalmiss, liger and seqtk, just type "make all" inside each directory.

To compile Minia3 you need CMake.

In the near future, I'm going to provide a conda package for wengan.

Best, Alex

[emmannaemeka]

I don't know what the problem is

intervalmiss]$ make all

mkdir obj

g++ -c -o obj/imopts.o src/imopts.cpp -O3 -std=c++11 -lpthread

g++ -c -o obj/MPCollection.o src/MPCollection.cpp -O3 -std=c++11 -lpthread

g++ -c -o obj/main.o src/main.cpp -O3 -std=c++11 -lpthread

g++ -c -o obj/MPLibrary.o src/MPLibrary.cpp -O3 -std=c++11 -lpthread

g++ -c -o obj/Finterval.o src/Finterval.cpp -O3 -std=c++11 -lpthread

g++ -c -o obj/Contig.o src/Contig.cpp -O3 -std=c++11 -lpthread

g++ -c -o obj/SAMR.o src/SAMR.cpp -O3 -std=c++11 -lpthread

g++ -o intervalmiss obj/imopts.o obj/MPCollection.o obj/main.o obj/MPLibrary.o obj/Finterval.o obj/Contig.o obj/SAMR.o -O3 -std=c++11 -lpthread

obj/Contig.o: In function `std::vector<std::string, std::allocator > splits(std::string const&, std::string const&)':

Contig.cpp:(.text.Z6splitsISsESt6vectorISsSaISsEERKSsRKT[Z6splitsISsESt6vectorISsSaISsEERKSsRKT]+0x87): undefined reference to `std::regex_token_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits

::regex_token_iterator(gnu_cxx::__normal_iterator<char const*, std::string>, gnu_cxx::__normal_iterator<char const*, std::string>, std::basic_regex<char, std::regex_traits > const&, int, std::bitset<11ul>)'

Contig.cpp:(.text.Z6splitsISsESt6vectorISsSaISsEERKSsRKT[Z6splitsISsESt6vectorISsSaISsEERKSsRKT]+0x94): undefined reference to `std::regex_token_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits >::regex_token_iterator()'

Contig.cpp:(.text.Z6splitsISsESt6vectorISsSaISsEERKSsRKT[Z6splitsISsESt6vectorISsSaISsEERKSsRKT]+0x111): undefined reference to `std::regex_token_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits >::operator++()'

Contig.cpp:(.text.Z6splitsISsESt6vectorISsSaISsEERKSsRKT[Z6splitsISsESt6vectorISsSaISsEERKSsRKT]+0x123): undefined reference to `std::regex_token_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits

::operator!=(std::regex_token_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits > const&)'

Contig.cpp:(.text.Z6splitsISsESt6vectorISsSaISsEERKSsRKT[Z6splitsISsESt6vectorISsSaISsEERKSsRKT]+0x135): undefined reference to `std::regex_token_iterator<__gnu_cxx::__normal_iterator<char const*, std::string>, char, std::regex_traits >::operator->()'

collect2: error: ld returned 1 exit status

make: *** [intervalmiss] Error 1

fastmin-sg]$ make all

cc -c -g -Wall -O3 -DHAVE_KALLOC -I ./minimap2 fastmin-sg.c -o fastmin-sg.o

fastmin-sg.c: In function 'revcomp':

fastmin-sg.c:94:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for (int i = 0; i < klen>>1; ++i) { // reverse complement sequence

• ^*

fastmin-sg.c:94:5: note: use option -std=c99 or -std=gnu99 to compile your code

fastmin-sg.c: In function 'maplongreads':

fastmin-sg.c:257:3: error: 'for' loop initial declarations are only allowed in C99 mode

for (int i = 0; i < libcount; ++i) headhits[i]=NULL;

• ^*

fastmin-sg.c:311:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i< rseq ; i++){ // each kseq_read() call reads one query

sequence

• ^*

fastmin-sg.c:313:6: error: 'for' loop initial declarations are only allowed in C99 mode

  for(int ii=0; ii<libcount; ii++){

• ^*

fastmin-sg.c:320:7: error: 'for' loop initial declarations are only allowed in C99 mode

   for(int l=0; l<max_d; l+=moving_w){

• ^*

fastmin-sg.c:388:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for (int f = 0; f < libcount; ++f)

• ^*

fastmin-sg.c:411:17: error: conflicting types for 'i'

 for (size_t i = 0; i < rseq; i++) {

• ^*

fastmin-sg.c:311:13: note: previous definition of 'i' was here

 for(int i=0; i< rseq ; i++){ // each kseq_read() call reads one query

sequence

• ^*

fastmin-sg.c:411:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for (size_t i = 0; i < rseq; i++) {

• ^*

fastmin-sg.c: In function 'map_long_read_files':

fastmin-sg.c:465:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i<libcount; i++){

• ^*

fastmin-sg.c:488:13: error: redefinition of 'i'

 for(int i =0; i < alnp->n_threads; ++i) tbuf[i] = mm_tbuf_init();

• ^*

fastmin-sg.c:465:13: note: previous definition of 'i' was here

 for(int i=0; i<libcount; i++){

• ^*

fastmin-sg.c:488:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i =0; i < alnp->n_threads; ++i) tbuf[i] = mm_tbuf_init();

• ^*

fastmin-sg.c:490:13: error: redefinition of 'i'

 for(int i=0; i < alnp->n_threads; i++){

• ^*

fastmin-sg.c:488:13: note: previous definition of 'i' was here

 for(int i =0; i < alnp->n_threads; ++i) tbuf[i] = mm_tbuf_init();

• ^*

fastmin-sg.c:490:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i < alnp->n_threads; i++){

• ^*

fastmin-sg.c:507:13: error: redefinition of 'i'

 for(int i=0; i< alnp->n_threads; ++i) pthread_join(tid[i], NULL);

• ^*

fastmin-sg.c:490:13: note: previous definition of 'i' was here

 for(int i=0; i < alnp->n_threads; i++){

• ^*

fastmin-sg.c:507:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i< alnp->n_threads; ++i) pthread_join(tid[i], NULL);

• ^*

fastmin-sg.c:509:13: error: redefinition of 'i'

 for(int i=0; i<alnp->n_threads; i++) mm_tbuf_destroy(tbuf[i]);

• ^*

fastmin-sg.c:507:13: note: previous definition of 'i' was here

 for(int i=0; i< alnp->n_threads; ++i) pthread_join(tid[i], NULL);

• ^*

fastmin-sg.c:509:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i<alnp->n_threads; i++) mm_tbuf_destroy(tbuf[i]);

• ^*

fastmin-sg.c:515:13: error: redefinition of 'i'

 for(int i=0; i<libcount ; i++){

• ^*

fastmin-sg.c:509:13: note: previous definition of 'i' was here

 for(int i=0; i<alnp->n_threads; i++) mm_tbuf_destroy(tbuf[i]);

• ^*

fastmin-sg.c:515:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i<libcount ; i++){

• ^*

fastmin-sg.c: In function 'rescue_pair':

fastmin-sg.c:532:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i<n_reg; i++){

• ^*

fastmin-sg.c: In function 'mapshortreads':

fastmin-sg.c:579:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for (int i = 0; i < libcount; ++i) headhits[i]=NULL;

• ^*

fastmin-sg.c:652:13: error: 'for' loop initial declarations are only allowed in C99 mode

         for(int i=0; i< rseq ; i++){ // each kseq_read() call reads

one query sequence

• ^*

fastmin-sg.c:759:13: error: 'for' loop initial declarations are only allowed in C99 mode

         for (int f = 0; f < libcount; ++f)

• ^*

fastmin-sg.c:789:25: error: conflicting types for 'i'

         for (size_t i = 0; i < rseq; i++) {

• ^*

fastmin-sg.c:652:21: note: previous definition of 'i' was here

         for(int i=0; i< rseq ; i++){ // each kseq_read() call reads

one query sequence

• ^*

fastmin-sg.c:789:13: error: 'for' loop initial declarations are only allowed in C99 mode

         for (size_t i = 0; i < rseq; i++) {

• ^*

fastmin-sg.c: In function 'infer_insert_size':

fastmin-sg.c:895:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i<1; i++) mm_tbuf_destroy(tbuf[i]);

• ^*

fastmin-sg.c:909:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for (int n=beg; n<end+1; n++) {

• ^*

fastmin-sg.c:917:14: error: redefinition of 'n'

 for (int n=beg; n<end+1; n++) {

• ^*

fastmin-sg.c:909:14: note: previous definition of 'n' was here

 for (int n=beg; n<end+1; n++) {

• ^*

fastmin-sg.c:917:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for (int n=beg; n<end+1; n++) {

• ^*

fastmin-sg.c: In function 'map_short_read_files':

fastmin-sg.c:990:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i =0; i < alnp->n_threads; ++i) tbuf[i] = mm_tbuf_init();

• ^*

fastmin-sg.c:992:13: error: redefinition of 'i'

 for(int i=0; i < alnp->n_threads; i++){

• ^*

fastmin-sg.c:990:13: note: previous definition of 'i' was here

 for(int i =0; i < alnp->n_threads; ++i) tbuf[i] = mm_tbuf_init();

• ^*

fastmin-sg.c:992:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i < alnp->n_threads; i++){

• ^*

fastmin-sg.c:1011:13: error: redefinition of 'i'

 for(int i=0; i< alnp->n_threads; ++i) pthread_join(tid[i], NULL);

• ^*

fastmin-sg.c:992:13: note: previous definition of 'i' was here

 for(int i=0; i < alnp->n_threads; i++){

• ^*

fastmin-sg.c:1011:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i< alnp->n_threads; ++i) pthread_join(tid[i], NULL);

• ^*

fastmin-sg.c:1013:13: error: redefinition of 'i'

 for(int i=0; i<alnp->n_threads; i++) mm_tbuf_destroy(tbuf[i]);

• ^*

fastmin-sg.c:1011:13: note: previous definition of 'i' was here

 for(int i=0; i< alnp->n_threads; ++i) pthread_join(tid[i], NULL);

• ^*

fastmin-sg.c:1013:5: error: 'for' loop initial declarations are only allowed in C99 mode

 for(int i=0; i<alnp->n_threads; i++) mm_tbuf_destroy(tbuf[i]);

• ^*

make: *** [fastmin-sg.o] Error

I don't know if anyone has thesame experiences.

Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Feb 10, 2020 at 10:59 AM adigenova notifications@github.com wrote:

The problem is that the pre-compiled binaries not found the required GLIB version (`GLIBCXX_3.4.21' not found). So, you have to re-compile from the sources.

the commands should be like this:

fetch Wengan and its components

git clone --recursive https://github.com/adigenova/wengan.git wengan

for each component, there are specific instructions.

I recommend to start building the WenganM pipeline, it requires the compilation of Minia3, fastmin-sg, intervalmiss, liger and seqtk.

To compile fastmin-sg, intervalmiss, liger and seqtk, just type "make all" inside each directory.

To compile Minia3 you need CMake.

In the near future, I'm going to provide a conda package for wengan.

Best, Alex

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/adigenova/wengan/issues/14?email_source=notifications&email_token=AHVLNZY7RUVWRISVRR2PREDRCEQPXA5CNFSM4KSERXO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELH4XVY#issuecomment-584043479, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ7PAT6XHPIXDLY6ZIDRCEQPXANCNFSM4KSERXOQ .

[adigenova]

Can you post the result of:

gcc --version g++ --version

It seems that you have an old GCC compiler.

best, Alex

[emmannaemeka]

gcc --version

gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)

Copyright (C) 2015 Free Software Foundation, Inc.

This is free software; see the source for copying conditions. There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE

g++ --version

g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)

Copyright (C) 2015 Free Software Foundation, Inc.

This is free software; see the source for copying conditions. There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Feb 10, 2020 at 12:20 PM adigenova notifications@github.com wrote:

Can you post the result of:

gcc --version g++ --version

It seems that you have an old GCC compiler.

best, Alex

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/adigenova/wengan/issues/14?email_source=notifications&email_token=AHVLNZ7YB6AU7LGAS7FUKQLRCEZ6FA5CNFSM4KSERXO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELIESPI#issuecomment-584075581, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ4VCRWNRQ3IKY3GAT3RCEZ6FANCNFSM4KSERXOQ .

[adigenova]

Ok, that is the problem , your C++ compiler is old, wengan was compilation was tested with:

with GCC version GCC/7.3.0-2.30 or higher.

So, to solve your issues, I recommend updating your GCC compiler (i.e > 7.)

Best, Alex

[emmannaemeka]

switched to

gcc (GCC) 7.3.1 20180303 (Red Hat 7.3.1-5)

Copyright (C) 2017 Free Software Foundation, Inc.

This is free software; see the source for copying conditions. There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE

but have this error

make: *** No targets specified and no makefile found. Stop.

Running simple test...

could not find a compiled Minia binary

Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Feb 10, 2020 at 12:31 PM adigenova notifications@github.com wrote:

Ok, that is the problem , your C++ compiler is old, wengan was compilation was tested with:

with GCC version GCC/7.3.0-2.30 or higher.

So, to solve your issues, I recommend updating your GCC compiler (i.e > 7.)

Best, Alex

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/adigenova/wengan/issues/14?email_source=notifications&email_token=AHVLNZ5X3BTAMLPVZZCPLOLRCE3J5A5CNFSM4KSERXO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELIFULA#issuecomment-584079916, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ6LOPIZAOM3LU7CRFTRCE3J5ANCNFSM4KSERXOQ .

[adigenova]

Great!!!, for compiling minia you have to run inside the directory:

# compile the code an run a simple test on your computer
cd minia
sh INSTALL

After compilation of all the components listed above, you have to copy them to ${ROOT_WENGAN}/bin.

best,

Alex

[emmannaemeka]

Followed this step

cd minia sh INSTALL

Cloning into 'thirdparty/gatb-core'...

remote: Enumerating objects: 8, done.

remote: Counting objects: 100% (8/8), done.

remote: Compressing objects: 100% (8/8), done.

remote: Total 29368 (delta 0), reused 3 (delta 0), pack-reused 29360

Receiving objects: 100% (29368/29368), 47.96 MiB | 23.36 MiB/s, done.

Resolving deltas: 100% (17999/17999), done.

Submodule path 'thirdparty/gatb-core': checked out '664696cbc3877d4eb6c3f10f87434efd4c0c83b4'

-- The C compiler identification is GNU 7.3.1

-- The CXX compiler identification is GNU 7.3.1

-- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc

-- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++

-- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

Git version: 5b131b9

-- gatb-core is here '/home/emmanuel/wengan/components/minia/thirdparty/gatb-core/gatb-core'

CMake Error at thirdparty/gatb-core/gatb-core/CMakeLists.txt:4 (cmake_minimum_required):

CMake 3.10.0 or higher is required. You are running version 2.8.12.2

-- Configuring incomplete, errors occurred!

See also "/home/emmanuel/wengan/components/minia/build/CMakeFiles/CMakeOutput.log".

make: *** No targets specified and no makefile found. Stop.

Running simple test...

could not find a compiled Minia binary

And still had same error

On Mon, 10 Feb 2020 at 2:23 PM, adigenova notifications@github.com wrote:

Great!!!, for compiling minia you have to run inside the directory: compile the code an run a simple test on your computer

cd minia sh INSTALL

After compilation of all the components listed above, you have to copy them to ${ROOT_WENGAN}/bin.

best,

Alex

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[adigenova]

The problem now is cmake, check this line in the log that you posted:

CMake 3.10.0 or higher is required. You are running version 2.8.12.2

update your cmake >= 3.1

best

[emmannaemeka]

As a quick fix I installed minia using conda and created a symbolic link in the wegan/bin folder. This seem to work

Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Feb 10, 2020 at 3:01 PM adigenova notifications@github.com wrote:

The problem now is cmake, check this line in the log that you posted: CMake 3.10.0 or higher is required. You are running version 2.8.12.2

update your cmake >= 3.1

best

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[adigenova]

OK, great!!!