package ncurses 5.9 fails to compile (gcc 7.4.0, ubuntu 18.04.3 LTS)

[FMKerckhof]

Dear, I am fairly new into the galaxy administration but a package that I am trying to install relies on ncurses 5.9. While I do get ncurses 6.0 installed without issues, I keep on getting errors when trying to install 5.9 through the toolshed. I am working with a "factory fresh" ubuntu 18.04.3 LTS server and the latest stable version of galaxy (19.05). I don't really understand what is the issue, since it should have been resolved and closed 4 years ago (#477). However, I get the following output:

Makefile:329: recipe for target '../obj_s/cursesf.o' failed
make[1]: Leaving directory '/home/username/galaxy/database/tmp/tmp-toolshed-mtdtO7pge/ncurses-5.9/c++'
Makefile:109: recipe for target 'all' failed
sername/galaxy/database/tmp/tmp-toolshed-mtdtO7pge/ncurses-5.9/lib  -I. -I. -I../test -DHAVE_CONFIG_xy/database/dependencies/
In file included from ../c++/cursesw.h:36:0,
                 from ../c++/cursesp.h:39,
                 from ../c++/cursesf.h:39,
                 from ../c++/cursesf.cc:35:
../c++/etip.h:374:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
 #define THROWS(s)  throw(s)
                    ^
../c++/cursesw.h:777:50: note: in expansion of macro ‘THROWS’
   virtual void   err_handler(const char *) const THROWS(NCursesException);
                                                  ^~~~~~
../c++/etip.h:374:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
 #define THROWS(s)  throw(s)
                    ^
../c++/cursesp.h:89:32: note: in expansion of macro ‘THROWS’
   void OnError (int err) const THROWS(NCursesPanelException)
                                ^~~~~~
In file included from ../c++/cursesf.h:39:0,
                 from ../c++/cursesf.cc:35:
../c++/cursesp.h: In member function ‘T* NCursesUserPanel<T>::UserData() const’:
../c++/cursesp.h:256:43: error: no matching function for call to ‘NCursesUserPanel<T>::get_user() const’
     return reinterpret_cast<T*>(get_user ());
                                           ^
../c++/cursesp.h:80:9: note: candidate: void* NCursesPanel::get_user() <near match>
   void *get_user()
         ^~~~~~~~
../c++/cursesp.h:80:9: note:   passing ‘const NCursesUserPanel<T>*’ as ‘this’ argument discards qualifiers
In file included from ../c++/cursesw.h:36:0,
                 from ../c++/cursesp.h:39,
                 from ../c++/cursesf.h:39,
                 from ../c++/cursesf.cc:35:
../c++/cursesf.h: At global scope:
../c++/etip.h:374:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
 #define THROWS(s)  throw(s)
                    ^
../c++/cursesf.h:64:38: note: in expansion of macro ‘THROWS’
   inline void OnError(int err) const THROWS(NCursesFormException) {
                                      ^~~~~~
../c++/etip.h:374:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
 #define THROWS(s)  throw(s)
                    ^
../c++/cursesf.h:112:39: note: in expansion of macro ‘THROWS’
   inline void OnError (int err) const THROWS(NCursesFormException) {
                                       ^~~~~~
../c++/etip.h:374:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
 #define THROWS(s)  throw(s)
                    ^
../c++/cursesf.h:394:39: note: in expansion of macro ‘THROWS’
   inline void OnError (int err) const THROWS(NCursesFormException) {
                                       ^~~~~~
In file included from ../c++/cursesf.cc:35:0:
../c++/cursesf.h: In member function ‘T* NCursesUserForm<T>::UserData() const’:
../c++/cursesf.h:707:43: error: no matching function for call to ‘NCursesUserForm<T>::get_user() const’
     return reinterpret_cast<T*>(get_user ());
                                           ^
../c++/cursesf.h:384:16: note: candidate: void* NCursesForm::get_user() <near match>
   inline void *get_user() {
                ^~~~~~~~
../c++/cursesf.h:384:16: note:   passing
*’ as ‘this’ argument discards qualifiers
In file included from ../c++/cursesw.h:36:0,
                 from ../c++/cursesp.h:39,
                 from ../c++/cursesf.h:39,
                 from ../c++/cursesf.cc:35:
../c++/cursslk.h: At global scope:
../c++/etip.h:374:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
 #define THROWS(s)  throw(s)
                    ^
../c++/cursslk.h:120:45: note: in expansion of macro ‘THROWS’
   inline void Error (const char* msg) const THROWS(NCursesException) {
                                             ^~~~~~
make[1]: *** [../obj_s/cursesf.o] Error 1
make: *** [all] Error 2
Updating an existing record for version 5.9 of tool dependency ncurses for revision 335ebf512407 of repository package_ncurses_5_9 by updating the status from Installing to Error.
Error installing tool dependency ncurses version 5.9: 'ascii' codec can't encode character u'\u2018' in position 191: ordinal not in range(128)
Traceback (most recent call last):
  File "lib/tool_shed/galaxy_install/install_manager.py", line 196, in install_specified_tool_dependencies
    from_tool_migration_manager=from_tool_migration_manager)
  File "lib/tool_shed/galaxy_install/install_manager.py", line 352, in install_package
    (str(package_name), str(package_version), str(tool_dependency.error_message)))
UnicodeEncodeError: 'ascii' codec can't encode character u'\u2018' in position 191: ordinal not in range(128)

Any help/pointers would be warmly welcomed.

Kind regards,

FM

[bgruening]

@FMKerckhof which tool is this? tool-shed packages are deprecated for years and you should not use them if you have the choice. Galaxy is using for a few years conda packages instead or containers.

[FMKerckhof]

Dear @bgruening thank you for getting back to me on such short notice, I am trying to use SNVphyl for the detection of single-nucleotide variants (https://snvphyl.readthedocs.io/en/latest/install/galaxy/). I am aware that there is a docker-cotainerized version available, but I am trying to integrate the tool with a pre-existing Galaxy install. I do not have conda installed on the system I think, could this be an issue?

[bgruening]

@FMKerckhof how old is this instance? Conda get automatically installed these days by Galaxy.

[FMKerckhof]

It is quite a fresh install (Galaxy 19.05), I just followed the "for production" instructions as they are now on https://galaxyproject.org/admin/get-galaxy/ . I meant that I do not have the conda command available in the OS, I am not sure if the galaxy itself has a version of conda available to it that I do not have system-wide (or if that is possible?).

[FMKerckhof]

So I have found out that is possible for me to use "install checked dependencies using conda" from the "manage dependencies menu". However, ncurses is not showing up as a dependency there.

[bgruening]

@FMKerckhof are you familiar with Conda? Conda is resolving the dependencies for you, e.g. ncurses gets installed automatically via Conda. So you do not need to worry about it. That said, this only works if you tool is using Conda packages.

ping @apetkau

[apetkau]

Thanks for tagging me @bgruening

@FMKerckhof we actually have an updated version of SNVPhyl available on the main Galaxy toolshed which uses all conda dependencies (https://toolshed.g2.bx.psu.edu/view/nml/suite_snvphyl_1_1_0/1f0f9b1b5580). We haven't quite gotten to updating our documentation yet. Sorry about that. Installing this newer version should hopefully resolve this (and other) issues.

Updated workflows for SNVPhyl can be found at https://github.com/phac-nml/snvphyl-galaxy/tree/development/docs/workflows/SNVPhyl/1.1.0.

[FMKerckhof]

Dear @apetkau thank you, that was exceptionally helpful. I still have a lot to learn on galaxy administration, but it appears I was able to install the tool and the dependencies (using conda). The workflows still give me the error "The data content does not appear to be a valid workflow." when I try to import them as workflow.

[jennaj]

Some help with troubleshooting:

This error is generated when the uploaded workflow (".ga" file) is not formatted correctly.

Line 605 here in the Galaxy core codebase: https://github.com/galaxyproject/galaxy/blob/release_19.05/lib/galaxy/webapps/galaxy/api/workflows.py

Maybe @apetkau can help more.

[apetkau]

Thanks @jennaj

@FMKerckhof how did you try importing the workflow? Was it via the URL? Could you specifically try this URL https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy/development/docs/workflows/SNVPhyl/1.1.0/snvphyl-workflow-1.1.ga

[FMKerckhof]

Dear @apetkau I tried donwloading and then uploading, but using the direct links to the raw github files indeed works. Thank you all (@bgruening & @jennaj too) for helping me with this!