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don't be lazy--RStudio Server's Upload button let me feel the desperation of genewise failure again

1 Perface

As for genewise, I don’t want to regret how much time I have wasted on it, neither do I need to complain how desperate and despaired I felt with it 1. I just want to make two points:

  1. biostars is really a good place, especially for tips on bioinformatics softwares. It was from there I found a practicable solution.

  2. Debian source package is always prefered to posts (from 百度经验 to StackOverflow).

2 Beginning

Back to the days I stay in Xie Lab, my research project heavily relies on HaMStR, which depends on genewise.

I tried numerous times, but still can’t build it from source. Luckily, apt provides a wise package. However, that means I won’t be able to use it on the CentOS workstation.

3 Development

Thanks to Debian source package so much. I finally find a way to build genewise from source, though it’s not quiet straightforward.

You need to download the Debian source package from here, the uncompass the downloaded two tarballs:

$ls
debian wise-2.4.1

Unfortunatelly, there is some inconsistency is the patch file. So you have to replace 2

--- a/
+++ b/

with

--- wise-2.4.1.orig/
+++ wise-2.4.1/

in 10_fix_path_to_data_files.patch and 11_consistent_manual_dates.patch 3.

Then, you can patch, build and enjoy:

for file in debian/patches/[01]*.patch; do patch -p0 < $file; done

cd wise-2.4.1/src
make all

4 Climax

I feel so happy and encouraged that I can’t wait to port it to the CentOS workstation.

But the good scene doesn’t last long. When I make on CentOS, I was told that dyc can’t be found. Oh, that error again, I return bakck to refer INSTALL of genewise, tried to make dyc with a tiny hope, watched it failed without any surprise.

To flog a dead horse, I Upload 4 the dyc file I made on Ubuntu. It complains about the permission so I chmod +x. Then it moved on till the final step, welcome.csh. I met the permission problem and do chmod +x again.

Though I get the binary executables, I wasn’t assured. So I tried the test program. Again, it failed. The is something wrong with the wisecfg/ location. Even if I set env variable WISECONFIGDIR, genewise still tried to search in /usr/share/wise 5. I don’t want to copy wisecfg directory to /usr/share/wise since I want to put genewise into ~/.local. Thus I turned to edit the source code, i.e., replace all /usr/share/wise with /home/user/.local/lib/wisecfg. This time everything is okay.

5 Epilogue

Succeed as I do, I still can’t feel relieved to rely on a binary executable made on Ubuntu to work on CentOS 6.

So, I start to think why this happens. The twice permission problems give me some clues. Then it dawned on me that the Upload button may break some files’ permission so that some command can’t be executed 7. Thus I make a .tar.gz and upload, uncompass. Finally I can 8 build genewise on CentOS!

By the way, I found even scp didn’t work the only solution is .tar.gz 9 .


  1. let alone the url in HaMStR README.txt should be http://www.ebi.ac.uk/~birney/wise2/ rather than http://www.ebi.ac.uk/~Ebirney/wise2/↩︎

  2. The above line is optional, but replacing both make it looks tidy.↩︎

  3. In the new version, there seem to be one more file: spelling.patch. Anyway, VSCode is a good choice, but remember to Save all after you finish the replacing.↩︎

  4. The Upload button in RStudio Server file explorer.↩︎

  5. It’s resonable since it’s a Debian package, and there is actually a wise-data package. But it bothers me.↩︎

  6. 真香!After make muscle failed on CentOS and Google it for about 30 minutes provides no solution, I copy the executable from Ubuntu.↩︎

  7. However, I think genewise should told me excatly where the error lie, like I wrote above, rather than dyc not found↩︎

  8. Of course I remembered to chmod -x ~/.local/bin/dyc to make sure I have solved the problem↩︎

  9. Actually I wasn’t a bit annoyed, instead I felt quiet at ease since the default compress way preserve many important feature thus save me many troubles.↩︎