refurbish installer for galaxyproject

[NCEichner]

Hi!

First of all sorry for bothering you on this channel but I don't find any opportunity to contact you on mercurial repository.
I would like to ask if there is a possibility to get the seqprep tool back on galaxy/galaxyproject?

Currently we're running the galaxy environment (release 17.09) on our server with Debian "stretch" (amd64). Here the present seqprep installer script errors in the 'make' command as follows:
`
SeqPrep.c: In function ‘main’:
SeqPrep.c:136:8: error: variable ‘print_overhang’ set but not used [-Werror=unused-but-set-variable]
bool print_overhang = false;
^~~~~~~~~~~~~~
SeqPrep.c: At top level:
SeqPrep.c:108:5: error: ‘spcount’ is static but used in inline function ‘update_spinner’ which is not static [-Werror]
spcount++;
^~~~~~~
SeqPrep.c:90:12: error: ‘spcount’ is static but used in inline function ‘update_spinner’ which is not static [-Werror]
switch(spcount % 4){
^~~~~~~
In file included from SeqPrep.c:10:0:
utils.h:79:13: error: inline function ‘rev_qual’ declared but never defined [-Werror]
inline void rev_qual( char q[], int len );
^~~~~~~~
utils.h:78:13: error: inline function ‘revcom_char’ declared but never defined [-Werror]
inline char revcom_char(const char base);
^~~~~~~~~~~
utils.h:62:13: error: inline function ‘f_r_id_check’ declared but never defined [-Werror]
inline bool f_r_id_check( char fid[], size_t fid_len, char rid[], size_t rid_len );
^~~~~~~~~~~~
utils.h:61:12: error: inline function ‘write_fastq’ declared but never defined [-Werror]
inline int write_fastq(gzFile out, char id[], char seq[], char qual[]);
^~~~~~~~~~~
utils.h:60:13: error: inline function ‘next_fastqs’ declared but never defined [-Werror]
inline bool next_fastqs( gzFile ffq, gzFile rfq, SQP curr_sqp, bool p64 );
^~~~~~~~~~~
utils.h:48:13: error: inline function ‘match_p33_merge’ declared but never defined [-Werror]
inline char match_p33_merge(char pA, char pB);
^~~~~~~~~~~~~~~
utils.h:47:13: error: inline function ‘mismatch_p33_merge’ declared but never defined [-Werror]
inline char mismatch_p33_merge(char pA, char pB);
^~~~~~~~~~~~~~~~~~
cc1: all warnings being treated as errors
make: *** [SeqPrep.o] Error 1

`
As this installation fails galaxy tries to install your tool via (ana)conda package manager. This takes version 1.2 of seqprep from bioconda and compiles this sucessfully to a working 'seqprep' executable. But somehow the remaining commands in the scriptfile "tool_dependencies.xml" are not properly executed by any installer. So "seqlens.py" is not copied to the desired folder and the environment file is not built. Finally Galaxy shows seqprep greyed out as installed but with missing dependencies.

In former installations we used some "repair repository" function, tweeked the installer script and merged the remnants of both install paths (Shed tool/mercurial and conda/bioconda) to somehow get your tool running. But this "repair" option seems to be dropped in the up-to-date version of galaxyproject. So after a neccessary reinstall of the galaxy instance we now are totally dependant on working tool installers.

I know that there are packages in the Debian repositories to get a globally installed seqprep for use with the commandline. But it would be great if we could go on using your tool within our galaxy workflows and in some situations for us seqprep is the only alternative inside or outside of the galaxy environment...

[jstjohn]

Hi there. So on my mac I see the warnings that your compiler is erroring out on only when I add COPTS=-Werror=unused-but-set-variable. Is it possible that you have some default COPTS or CFLAGS set in your ENV? If so you could try this, which should override your system ENV defaults:

make COPTS="" CFLAGS="-c -Wall -O3 -std=c99"

[jstjohn]

Of course the best option would be to actually address unused variables in code, but this should get you going :)

[jstjohn]

Also I see more warnings when I use gcc-7 over clang. My compilation works (with warnings) with gcc-7 when I set that as the CC as well:

make CC=gcc-7 COPTS="" CFLAGS="-c -Wall -O3 -std=c99"

[NCEichner]

Thanks for your answers and sorry for the delay. I just came back from winter holiday.

After some testing I think the basic problem is not located in the COPTS and CFLAGS but in the install script of the galaxy wrapper and the missing "repair repository"-button within the current version of the galaxy environment. (This missing button I will adress at the Galaxy github community seperately.)

So as I told before at the moment I only can execute 'install' or 'uninstall'. If the install script for the tool wrapper in galaxy is not working for some reason I am no longer able to edit the "tool-dependencies.xml" (e.g. for changing parameters in the make command) and then rerun the install script via the "repair repository" button.

I checked the stats of the seqprep wapper. It was written by someone named "lionelguy". The repository of the wrapper files is located at https://toolshed.g2.bx.psu.edu/repos/lionelguy/seqprep.
There's a scientist named Lionel Guy currently working in sweden who could be the author and I even found some eMail adress but I'm not completely sure. Did this person contact you while writing his wrapper software?

Btw.:
The decisive step in the install script seems to be the reset command:
git reset --hard 11301c4a5f3222bdb4d0ec30ae5e192e609c0154
When I execute the commands from this script one by one in a seperate test situation apart from the galaxy environment and skip this 'reset' command then I get an executable "seqprep" file (with 4 warnings but no errors) just by executing 'make' without any parameters.

[jstjohn]

Huh, yeah you could change that line to match the current master git hash, that way you will still be locking the version but updating it to one that apparently compiles for you at least.

…

On Mon, Jan 8, 2018 at 10:52 AM Norbert Eichner ***@***.***> wrote: Thanks for your answers and sorry for the delay. I just came back from winter holiday. After some testing I think the basic problem is not located in the COPTS and CFLAGS but in the install script of the galaxy wrapper and the missing "repair repository"-button within the current version of the galaxy environment. (This missing button I will adress at the Galaxy github community seperately.) So as I told before at the moment I only can execute 'install' or 'uninstall'. If the install script for the tool wrapper in galaxy is not working for some reason I am no longer able to edit the "tool-dependencies.xml" (e.g. for changing parameters in the make command) and then rerun the install script via the "repair repository" button. I checked the stats of the seqprep wapper. It was written by someone named "lionelguy". The repository of the wrapper files is located at https://toolshed.g2.bx.psu.edu/repos/lionelguy/seqprep. There's a scientist named Lionel Guy currently working in sweden who could be the author and I even found some eMail adress but I'm not completely sure. Did this person contact you while writing his wrapper software? Btw.: The decisive step in the install script seems to be the reset command: git reset --hard 11301c4 When I execute the commands from this script one by one in a seperate test situation apart from the galaxy environment and skip this 'reset' command then I get an executable "seqprep" file (with 4 warnings but no errors) just by executing 'make' without any parameters. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#42 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAcBBmUto8dNcMbQaas98Kvjqq-DezlQks5tImPqgaJpZM4RHZvD> .