Error with ncurses 5.9

[PHemarajata]

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"?> <tool_dependency> <package name="ncurses" version="5.9"> <install version="1.0"> <actions_group> <actions os="linux" architecture="x86_64"> <action type="download_by_url" md5sum="8cb9c412e5f2d96bc6f459aa8c6282a1">http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz</action> <action type="shell_command"> wget https://raw.githubusercontent.com/cloudius-systems/osv/07e2d9032dbb3f4f2b0d0133e0eccd5be05dd05d/modules/ncurses/ncurses-5.9-gcc-5.patch &amp;&amp; patch ncurses/base/MKlib_gen.sh ncurses-5.9-gcc-5.patch </action> <action type="autoconf">--with-shared --enable-symlinks</action> </actions> <actions os="darwin" architecture="x86_64"> <action type="download_by_url" md5sum="8cb9c412e5f2d96bc6f459aa8c6282a1">http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz</action> <action type="autoconf">--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</action> </actions> <action type="set_environment"> <environment_variable action="set_to" name="NCURSES_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> <environment_variable action="set_to" name="NCURSES_LIB_PATH">$INSTALL_DIR/lib/</environment_variable> <environment_variable action="set_to" name="NCURSES_ROOT_PATH">$INSTALL_DIR</environment_variable> <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> <environment_variable action="prepend_to" name="DYLD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> <environment_variable action="prepend_to" name="LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> </action> </actions_group> </install> <readme> 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 </readme> </package> </tool_dependency>

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]

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

[apetkau]

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]

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]

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

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

[PHemarajata]

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

Thank you!

[apetkau]

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.