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 notifications@github.com 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.

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[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.