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phac-nml / snvphyl-galaxy

SNVPhyl whole genome phylogenomics pipeline.
Apache License 2.0
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Error with ncurses 5.9 #16

Open PHemarajata opened 5 years ago

PHemarajata commented 5 years ago

Hi! I am installing SNVPhyl on Galaxy 19.05 and went about fixing the known make error with a new tool dependencies xml below: `<?xml version="1.0"?>

http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz wget https://raw.githubusercontent.com/cloudius-systems/osv/07e2d9032dbb3f4f2b0d0133e0eccd5be05dd05d/modules/ncurses/ncurses-5.9-gcc-5.patch && patch ncurses/base/MKlib_gen.sh ncurses-5.9-gcc-5.patch --with-shared --enable-symlinks http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz --with-shared --enable-symlinks --without-cxx --without-cxx-binding --without-ada --without-progs --without-curses-h --without-debug --enable-widec --enable-const --enable-ext-colors --enable-sigwinch --enable-wgetch-events $INSTALL_DIR/include $INSTALL_DIR/lib/ $INSTALL_DIR $INSTALL_DIR/lib $INSTALL_DIR/lib $INSTALL_DIR/lib $INSTALL_DIR/include $INSTALL_DIR/include ncurses (new curses) is a programming library that provides an API which allows the programmer to write text-based user interfaces in a terminal-independent manner ` However, I ran into a new problem when reinstalling ncurses: ` Error installing tool dependency ncurses version 5.9: 'ascii' codec can't encode character u'\u2018' in position 251: ordinal not in range(128)` I would really appreciate any suggestion on how to fix this. Thank you!
PHemarajata commented 5 years ago

I am so sorry the formatting of the code in the post is all wrong!

apetkau commented 5 years ago

That's okay about formatting.

So, I have not seen that specific error before. You could try installing ncurses through your system package manager (apt or yum). The exact version I don't think matters so much, this was just the version available in Galaxy as a dependency when those tools were written.

Note that we are nearing completion of a release of SNVPhyl that will use conda to install dependencies (rather than the older methods used by Galaxy) - #15 . So, this issue should hopefully go away fairly soon.

PHemarajata commented 5 years ago

Hi. Thank you so much for the response! I had ncurses installed via apt, but how do I make Galaxy know where it is so the dependencies error goes away?

Can't wait to use a version utilizing CONDA.

apetkau commented 5 years ago

You can disable/uninstall ncurses in Galaxy by going to Admin > Manage tools, selecting package_ncurses_5_9 and uninstalling it from Galaxy.

image

If ncurses is available on the machine Galaxy is running the tools on it should just use the system version instead.

PHemarajata commented 5 years ago

I am so excited about the version utilizing conda! Any idea when it'd be released?

Thank you!

apetkau commented 5 years ago

It's available on the Main Galaxy Toolshed right now (https://toolshed.g2.bx.psu.edu/view/nml/suite_snvphyl_1_1_0/1f0f9b1b5580). And updated workflows are available at https://github.com/phac-nml/snvphyl-galaxy/tree/development/docs/workflows/SNVPhyl/1.1.0. We just haven't gotten our documentation all updated.