Difficulty installing fastx_toolkit on MAC

Question

[jaqx008]

Hey everyone, I am having challenges installing fast_toolkit on my mac. I have tried many suggestions like downloading it and performing make, configure etc on terminal. It has not yielded any good result. I don't know what Im doing wrong? Can someone help please? Thanks below is the last command I ran if it may help.

$ make
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in m4
make[2]: Nothing to be done for `all'.
Making all in src
Making all in libfastx
gcc -DHAVE_CONFIG_H -I. -I../..     -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx.o -MD -MP -MF .deps/fastx.Tpo -c -o fastx.o fastx.c
In file included from fastx.c:19:
In file included from /usr/include/stdlib.h:65:
In file included from /usr/include/sys/wait.h:110:
/usr/include/sys/resource.h:196:2: error: unknown type name 'uint8_t'
        uint8_t  ri_uuid[16];
        ^
/usr/include/sys/resource.h:197:2: error: unknown type name 'uint64_t'
        uint64_t ri_user_time;
        ^
/usr/include/sys/resource.h:198:2: error: unknown type name 'uint64_t'
        uint64_t ri_system_time;
        ^
/usr/include/sys/resource.h:199:2: error: unknown type name 'uint64_t'
        uint64_t ri_pkg_idle_wkups;
        ^
/usr/include/sys/resource.h:200:2: error: unknown type name 'uint64_t'
        uint64_t ri_interrupt_wkups;
        ^
/usr/include/sys/resource.h:201:2: error: unknown type name 'uint64_t'
        uint64_t ri_pageins;
        ^
/usr/include/sys/resource.h:202:2: error: unknown type name 'uint64_t'
        uint64_t ri_wired_size;
        ^
/usr/include/sys/resource.h:203:2: error: unknown type name 'uint64_t'
        uint64_t ri_resident_size;
        ^
/usr/include/sys/resource.h:204:2: error: unknown type name 'uint64_t'
        uint64_t ri_phys_footprint;
        ^
/usr/include/sys/resource.h:205:2: error: unknown type name 'uint64_t'
        uint64_t ri_proc_start_abstime;
        ^
/usr/include/sys/resource.h:206:2: error: unknown type name 'uint64_t'
        uint64_t ri_proc_exit_abstime;
        ^
/usr/include/sys/resource.h:210:2: error: unknown type name 'uint8_t'
        uint8_t  ri_uuid[16];
        ^
/usr/include/sys/resource.h:211:2: error: unknown type name 'uint64_t'
        uint64_t ri_user_time;
        ^
/usr/include/sys/resource.h:212:2: error: unknown type name 'uint64_t'
        uint64_t ri_system_time;
        ^
/usr/include/sys/resource.h:213:2: error: unknown type name 'uint64_t'
        uint64_t ri_pkg_idle_wkups;
        ^
/usr/include/sys/resource.h:214:2: error: unknown type name 'uint64_t'
        uint64_t ri_interrupt_wkups;
        ^
/usr/include/sys/resource.h:215:2: error: unknown type name 'uint64_t'
        uint64_t ri_pageins;
        ^
/usr/include/sys/resource.h:216:2: error: unknown type name 'uint64_t'
        uint64_t ri_wired_size;
        ^
/usr/include/sys/resource.h:217:2: error: unknown type name 'uint64_t'
        uint64_t ri_resident_size;
        ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[3]: *** [fastx.o] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

[GenoMax]

Which tool from fastx_toolkit are you interested in using? fastx_toolkit has not been updated in a long while and you may want to go with a current software option instead.

[h.mon]

The best advice is to use newer, more current tools - in particular do not use FastX_toolkit with paired-end data. However, if you really want to install it, why not use homebrew or conda?

[jaqx008]

Yes. I tried to use brew to install it also just incase the need for any of the tool may arise soon. but brew won't install it

[joselatran]

Why not use it with paired-end data? Do you have a reference to explain that?

[jaqx008]

Im interested in using the fast_clipping tool. Is there a way I can install just this tool via terminal?

[GenoMax]

Use bbduk.sh from BBMap suite instead. Guide for bbduk can be found here.

[jaqx008]

Ok. let me try that

[jaqx008]

Thanks for your contribution. I was able to resolve it with my boss. we used one tool at a time and it worked fine. again. Thanks

[igor]

Have you tried using the pre-compiled binaries?

[jaqx008]

I tried but I think I am not calling the command properly or something

[igor]

If you have a problem calling a command, compiling is a much greater challenge.

How are you calling it and what is the error?

[jaqx008]

I realized the tool isn't in my path. the fastx_clipper works if i drag the entire tool(path) into my command. Thanks for your help