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Hey guys, I've been a windows user all my life. This summer I've had to do some bioinformatics for a biology lab I'm working in, and have to run lots ...
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  1. #1
    Just Joined!
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    Jun 2013
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    7

    Total Nub Trying to Install ViennaRNA package


    Hey guys,

    I've been a windows user all my life. This summer I've had to do some bioinformatics for a biology lab I'm working in, and have to run lots of data locally on my machine. These bioinformatics programs are available for download, and when I tried to install them, I was like WTF?

    I had never seen a set of files I had to 'compile from source' before. So I hunted around and realized I had to install Linux. So I dual-booted my PC, and here I am on the other side typing this.

    I've been trying to install this program:

    Vienna RNA Package
    (I can't post the link cause they have a spam filter thing. You'll have to google it)

    And have had 0 luck because I understand 0 about Linux.

    Here's where I am.

    I type

    ./configure
    ...
    make
    ...
    make install

    And get an error that I need some sort of GCC compiler.
    I go and download the GCC compiler, and do the same

    Code:
    ./configure
    make
    make install
    I get an error that I need three other programs
    GMP, MPC, and MPFR

    I go and download these three things and I THINK I successfully installed GMP and MPFR (I did the same thing,

    Code:
    ./configure
    make
    make install
    )

    But a nub like me likes to see confirmation messages.

    Anyways, when installing MPC, I get the error:

    Code:
    configure: error: no termcap library found
    make[2]: *** [configure-gdb] Error 1
    make[2]: Leaving directory `/home/nick/Downloads/MPC_2.4.1/mpc-gdb-6.8_build'
    make[1]: *** [all] Error 2
    make[1]: Leaving directory `/home/nick/Downloads/MPC_2.4.1/mpc-gdb-6.8_build'
    make: *** [mpc-gdb-6.8_make] Error 2
    And I found that I then needed something called ncurses.

    I went and downloaded that, and got another effing error:

    Code:
    /bin/sh: 1: -I../c++: not found
    make[1]: *** [../objects/cursesf.o] Error 127
    make[1]: Leaving directory `/home/nick/Downloads/ncurses-5.9/c++'
    make: *** [all] Error 2

    Essentially I'm just lost and running around like a chicken with its head cut off. I have no idea why these installations have to be carried out the way they do. I'm essentially knowledgeless on Linux.

    So I guess my question is:

    a) What do I need to do to get this package (ViennaRNA above) installed on my PC?
    b) Can someone explain the jist of why someone would choose to use Linux over Windows when these installations are filled with errors and much more complicated (I realize I seem ignorant, I'm just frustrated right now).

    Cheers,
    Nick

  2. #2
    Just Joined!
    Join Date
    Jun 2013
    Posts
    7
    Sorry for the double post, but now I'm trying to install RNA Hybrid (a different bioinformatics program)

    I do the same thing----

    Download
    Extract
    Open the extracted folder
    Right click --> Open in terminal, type

    ./configure
    make
    make install

    (I do this as superuser btw.)

    And don't get any error messages (at least I don't think)

    Here's my terminal log. Does this look correct? If not, what do I need to do? And if so, where does the program install to so I can use it?

    Code:
    linuxmint RNAhybrid-2.1.1 # ./configure
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for gawk... gawk
    checking whether make sets $(MAKE)... yes
    checking for gcc... gcc
    checking for C compiler default output... a.out
    checking whether the C compiler works... yes
    checking whether we are cross compiling... no
    checking for suffix of executables... 
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ANSI C... none needed
    checking for style of include used by make... GNU
    checking dependency style of gcc... gcc3
    checking for log in -lm... yes
    checking for g2_open_vd in -lg2... no
    configure: WARNING: libg2.a is missing. You can download it at ...
    checking for gdImageLine in -lgd... no
    checking how to run the C preprocessor... gcc -E
    checking for egrep... grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking g2.h usability... no
    checking g2.h presence... no
    checking for g2.h... no
    checking g2_PS.h usability... no
    checking g2_PS.h presence... no
    checking for g2_PS.h... no
    checking for an ANSI C-conforming const... yes
    checking for inline... inline
    checking for size_t... yes
    configure: creating ./config.status
    config.status: creating Makefile
    config.status: creating src/Makefile
    config.status: creating man/Makefile
    config.status: creating config.h
    config.status: config.h is unchanged
    config.status: executing depfiles commands
    linuxmint RNAhybrid-2.1.1 # make
    make  all-recursive
    make[1]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1'
    Making all in src
    make[2]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1/src'
    make[2]: Nothing to be done for `all'.
    make[2]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1/src'
    Making all in man
    make[2]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1/man'
    make[2]: Nothing to be done for `all'.
    make[2]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1/man'
    make[2]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1'
    make[2]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1'
    make[1]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1'
    linuxmint RNAhybrid-2.1.1 # make install
    Making install in src
    make[1]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1/src'
    make[2]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1/src'
    /bin/bash ../mkinstalldirs /usr/local/bin
      /usr/bin/install -c RNAhybrid /usr/local/bin/RNAhybrid
      /usr/bin/install -c RNAcalibrate /usr/local/bin/RNAcalibrate
      /usr/bin/install -c RNAeffective /usr/local/bin/RNAeffective
    make[2]: Nothing to be done for `install-data-am'.
    make[2]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1/src'
    make[1]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1/src'
    Making install in man
    make[1]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1/man'
    make[2]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1/man'
    make[2]: Nothing to be done for `install-exec-am'.
    /bin/bash ../mkinstalldirs /usr/local/man/man1
     /usr/bin/install -c -m 644 ./RNAhybrid.1 /usr/local/man/man1/RNAhybrid.1
     /usr/bin/install -c -m 644 ./RNAcalibrate.1 /usr/local/man/man1/RNAcalibrate.1
     /usr/bin/install -c -m 644 ./RNAeffective.1 /usr/local/man/man1/RNAeffective.1
    make[2]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1/man'
    make[1]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1/man'
    make[1]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1'
    make[2]: Entering directory `/home/nick/Downloads/RNAhybrid-2.1.1'
    make[2]: Nothing to be done for `install-exec-am'.
    make[2]: Nothing to be done for `install-data-am'.
    make[2]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1'
    make[1]: Leaving directory `/home/nick/Downloads/RNAhybrid-2.1.1'
    linuxmint RNAhybrid-2.1.1 #
    Thanks again,

    Nick

  3. #3
    Penguin of trust elija's Avatar
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    Posts
    3,482
    To install all your compilers and associated libraries simply by running
    Code:
    sudo apt-get install build-essential
    or you can search through the software centre. It may also be worth checking for binaries of your software in there. Although if compiling, anything that configure throws up such as libg2.a in your example should be installable through there also.

    Phew!
    What do we want?
    Time machines!

    When do we want 'em?
    Doesn't really matter does it!?


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  4. #4
    Just Joined!
    Join Date
    Jun 2013
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    7
    Fantastic!

    I'm on my Windows OS right now, and I think I got RNAHybrid up and running so I'm just compiling my data to run in that program.
    Once I switch over, I'll try what you said and let y'all know how it worked out.

    Thanks for the quick reply!

    Reg

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