mfold-3.6

http://www.unafold.org/mfold/software/download-mfold.php

Prerequisites:

• Ubuntu
  • Install gfortran, g++, make
  • Download mfold, gs src

Howto build

• Ubuntu
  • mfold
    • _{^{chmod 744 ./configure}}
    • FFLAGS="-static-libgfortran -static-libgcc -static" LDFLAGS="-static" ./configure --prefix=/root/mfold/mfold-3.6 --disable-dependency-tracking
    • Rename src/UGENEefn.f and src/UGENEnewtemp.f to src/efn.f and src/newtemp.f consequently (yes, rewrite files generated by configure) (cp src/UGENEefn.f src/efn.f, cp src/UGENEnewtemp.f src/newtemp.f)
    • Run make, then make install
    • After make install there is a folder /root/mfold/mfold-3.6/bin with scripts and binaries. Replace /root/mfold/mfold-3.6/bin/mfold with ./UGENEmfold (rename it to mfold) (cp UGENEmfold /root/mfold/mfold-3.6/bin/mfold)
    • Finally copy UGENE proxy et-like script for calling mfold: cp UGENEmfold.sh /root/mfold/mfold.sh
  • gs
    • CXXFLAGS="-std=c++98" LDFLAGS=-static ./configure --prefix=/root/mfold/gs10.02.0 --with-libiconv=no --without-libtiff --without-ijs --without-urf --without-so --without-cal --with-drivers=PNG,PS --without-gnu-make --with-fontpath --without-tesseract --disable-fontconfig
    • make && make install
    • (Optionally) Remove doc and man folders from gs prefix folder.
  • (Optionally) Check correctness:
    • echo TAGTTATTAATAGTA > inp.txt
    • _{^{chmod 744 /root/mfold/mfold.sh}}
    • /root/mfold/mfold.sh SEQ=inp.txt NA=DNA
    • Expected: script finished successfully, a lot of files started with "inp.txt" generated, there are 11 ps files and 11 png files.
    • ldd /root/mfold/mfold-3.6/bin/auxgen shouldn't print shared/dinamic libraries.
    • ldd /root/mfold/gs10.02.0/bin/gs shouldn't print shared/dinamic libraries.

Note that this check isn't enough.

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Todo

• Add chmod for scripts in git
• -std=c++98 or -static? Why is this enough? Where is the difference?
• Spaces in path don't work