emC_autoAlign.sh missing in compiled files

[yuanhaowang1213]

I wanted to compile emClarity. I added 'emC_ctfFind' to the mexFiles/compiled, however, it seems that there is still a missing file, 'emC_autoAlign.sh' in the folder according to 'mCompiled.sh' file.

[bHimes]

Which branch are you hoping to compile? I've just changed how these things work, so my reply will depend that info. Happy to help though, just let me know. Ben

…

On Mon, Apr 20, 2020, 3:48 PM Yuanhao Wang ***@***.***> wrote: I wanted to compile emClarity. I added 'emC_ctfFind' to the mexFiles/compiled, however, it seems that there is still a missing file, 'emC_autoAlign.sh' in the folder according to 'mCompiled.sh' file. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#117>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAXPLGAZRDPXHXRNCER6ILDRNSRKJANCNFSM4MMW7YXA> .

[yuanhaowang1213]

Dear Ben,
It was the code on the git repository, 'https://github.com/bHimes/emClarity'. I just cloned to my local file folder. I could download the emC_ctFind from you link in wiki, but could not find the emC_autoAlign.sh file.
Best,
yuanhao

[bHimes]

Hi Yuanhao, please try to use the LTS_version_1_5_0 branch. If you look there, you will see that the script is moved to the alignment direcotry, and there is also a emC_findBeads script.

[yuanhaowang1213]

Dear Ben,
The LTS_version link only contains the executable files. Still no directory.
Best,
Yuanhao

[bHimes]

Did you change to the LTS BRANCH of the source code?

[yuanhaowang1213]

Dear Ben,
Thank you. However, there is another issue that, in the ./testScripts/mCompile.sh file. Line 8, there is an

export emC_DEPS="/groups/grigorieff/home/himesb/work/emC_dependencies"

However, it seems that this folder is missing on the github or wiki link.

Best,

[bHimes]

It is there (link to google drive) but it is on the [[requirements|Requirements]] page. I added a link from the [[installation|Installation]] page to make it more clear. Sorry for the confusion. This part of the code is in a bit of flux, because I am preparing to also include statically linked imod binaries as well.