search

torognes / swarm

A robust and fast clustering method for amplicon-based studies
GNU Affero General Public License v3.0
121 stars 23 forks source link

Installation issues #159

Closed naurasd closed 3 years ago

naurasd commented 3 years ago

Hi,

trying to install swarm but get the following error when trying to run make:

make -C src swarm make[1]: Entering directory 'C:/Users/Nauras/swarm/src' g++ -g -flto -O3 -march=x86-64 -mtune=generic -std=c++11 -Wall -Wextra -pedantic -c -o swarm.o swarm.cc process_begin: CreateProcess(NULL, g++ -g -flto -O3 -march=x86-64 -mtune=generic -std=c++11 -Wall -Wextra -pedantic -c -o swarm.o swarm.cc, ...) failed. make (e=2): Das System kann die angegebene Datei nicht finden. make[1]: *** [<builtin>: swarm.o] Error 2 make[1]: Leaving directory 'C:/Users/Nauras/swarm/src' make: *** [Makefile:30: bin/swarm] Error 2

Any idea what the problem could be?

Cheers Nauras

naurasd commented 3 years ago

Apparently, swarm.o cannot be found. It doesn't exist in the swarm/src directory (swarm.cc does).

frederic-mahe commented 3 years ago

Hi @naurasd

we provide swarm binaries for Windows users (see releases), but I think @torognes uses MinGW to cross-compile from a GNU/Linux system. So, you might need to modify swarm's Makefile if you want to compile directly on a Windows system. Maybe Torbjørn can comment on that?

naurasd commented 3 years ago

Yeah I downloaded the binaries for swarm3.0.0. It was basicaly just a bin folder with swarm.exe. Running this lead to the following:

Waiting for data... (Hit Ctrl-C and run swarm -h if you meant to read data from a file.)

What file is needed here?

lczech commented 3 years ago

That looks good, so it is running then! Now you need to use the command line to invoke swarm in a way that actually processes data, see the README and/or read the manual.

frederic-mahe commented 3 years ago

swarm is waiting for input data, usually a fasta file of dereplicated amplicon sequences. Something like this:

>s1_14
ACGTACGT
>s2_2
TCGTACGT
...

but slightly different input formats are also possible (see swarm's help).

naurasd commented 3 years ago

thanks for the replies, but I am a bit confused. The binary folder contained the exe file. So that means I can run swarm via this file without the need to actually compile it via the make command?

torognes commented 3 years ago

Yes, the binary (exe file) is provided for your convenience.

naurasd commented 3 years ago

I like the convenient option :-D thanks for the help guys