Question: Difficulty installing fastx_toolkit on MAC
0
gravatar for jaqx008
10 months ago by
jaqx00840
jaqx00840 wrote:

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
ADD COMMENTlink modified 10 months ago by genomax63k • written 10 months ago by jaqx00840
1

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.

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax63k

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?

ADD REPLYlink written 10 months ago by h.mon24k

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

ADD REPLYlink written 10 months ago by jaqx00840

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

ADD REPLYlink modified 10 months ago • written 10 months ago by jaqx00840

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

ADD REPLYlink written 10 months ago by genomax63k

Ok. let me try that

ADD REPLYlink written 10 months ago by jaqx00840

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

ADD REPLYlink written 10 months ago by jaqx00840

Have you tried using the pre-compiled binaries?

ADD REPLYlink written 10 months ago by igor7.4k

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

ADD REPLYlink written 10 months ago by jaqx00840

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

How are you calling it and what is the error?

ADD REPLYlink written 10 months ago by igor7.4k

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

ADD REPLYlink written 10 months ago by jaqx00840
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