Option to make wrapper script executable for others

[gq1]

Currently the wrapper script is only executable for the owner.
-rwxr--r-- 1 tolsoft toladmin 478 Mar 14 19:57 samtools

Can we have an option to make them executable for others?
I made the following changes:

diff --git a/shpc/utils/fileio.py b/shpc/utils/fileio.py
index b8c5bb30f..061e3f424 100644
--- a/shpc/utils/fileio.py
+++ b/shpc/utils/fileio.py
@@ -123,7 +123,7 @@ def write_file(filename, content, mode="w", exec=False):
         filey.writelines(content)
     if exec:
         st = os.stat(filename)
-        os.chmod(filename, st.st_mode | stat.S_IEXEC)
+        os.chmod(filename, st.st_mode | stat.S_IXOTH)
     return filename

[muffato]

I understand the issue with S_IEXEC, which is a synonym of S_IXUSR according to https://docs.python.org/3/library/stat.html , but S_IXOTH in theory only sets the bits for the others. What about using S_IXUSR | S_IXGRP | S_IXOTH to guarantee that everyone can execute it ?

[gq1]

@muffato Yes, that is right.

Because I just updated the installation, the scripts already there, each time it just added the bit.

-        os.chmod(filename, st.st_mode | stat.S_IEXEC)
+        os.chmod(filename, st.st_mode | stat.S_IEXEC | stat.S_IXGRP | stat.S_IXOTH)

[vsoch]

This looks great! Would you be able to open a PR to fix it? And make sure to: 1. bump the changelog and add a node, and 2. bump the version to the corresponding change in shpc/version.py. Thank you!

[vsoch]

Actually it's before the work day, I can throw in a quick PR if you can review. Thanks!

[vsoch]

@gq1 and @muffato please check out #513 it should have your fixes!

[gq1]

Thanks @vsoch

[muffato]

Thank you @vsoch !