How do I install APT-MIDAS on linux command line?

Question

[melissachua90]

I want to use a specific APT program/application on linux, ie apt-midas.

The APT tools can be found here: https://media.affymetrix.com/support/developer/powertools/changelog/index.html

I've installed APT using wget but apt-midas cannot be found. How do I install apt-midas?

[massa.kassa.sc3na]

You need to make sure, that the apt-midas is accessible (that means found in PATH).

Basically, there are 2 ways:

1) Copy the binaries to location already in PATH (what is in PATH can be viewed with echo $PATH)

2) Add the directory with the binaries to PATH (described many times on the web, e.g. here https://linuxize.com/post/how-to-add-directory-to-path-in-linux/)

GL

[melissachua90]

I used this export PATH=$PWD:$PATH command but still am unable to access apt-midas.

[massa.kassa.sc3na]

Have you verified that the PATH has been set? And, more importantly, were you located in the unpacked directory with the midas binaries? The export is also one-time setting only.

Also note, that there is a bin directory, which is the directory that you need to add.

One more thing, I've noticed, that on my systems, the binaries were not executable automatically, I've had to use chmod +x apt-midas (replace the apt-midas with the program of your choice) to make them executable.

Could you post the command outputs if it still doesn't work?

[melissachua90]

The commands that I ran

wget https://downloads.thermofisher.com/APT/APT_2.11.3/apt_2.11.3_linux_64_bit_x86_binaries.zip

 unzip apt_2.11.3_linux_64_bit_x86_binaries.zip


chmod -R 775 apt_2.11.3_linux_64_bit_x86_binaries

export PATH="$HOME/bin:$PATH"

cd apt_2.11.3_linux_64_bit_x86_binaries/doc/

The apt-midas.html file can be located in the directory but I wasn't able to call it with apt-midas.

[massa.kassa.sc3na]

This sequence of commands will not work.

Do this:

wget https://downloads.thermofisher.com/APT/APT_2.11.3/apt_2.11.3_linux_64_bit_x86_binaries.zip # download
unzip apt_2.11.3_linux_64_bit_x86_binaries.zip # unpack
cd apt_2.11.3_linux_64_bit_x86_binaries/bin # go inside the bin directory
chmod +x * # make all files executable
export PATH=$PWD:$PATH # add current path to PATH (ONE TIME ONLY)

[melissachua90]

Thanks! I managed to launch apt-midas.

However, I want to run the following

## APT
#midas p-values (exon array)
$ cd apt_2.11.3_linux_64_bit_x86_binaries/bin/
> --cel-files /home/melissachua/adv_genomics/output-dir/celfiles.txt \
> -g /home/melissachua/adv_genomics/output-dir/gene/gene-rma-sketch.summary.txt \
> -e /home/melissachua/adv_genomics/output-dir/exon/exon-rma-sketch.summary.txt \
> -m /home/melissachua/adv_genomics/output-dir/HuEx-1_0-st-v2.r2.dt1.hg18.full.mps \
> -f \
> -n \
> --no-logtrans \
> -o /home/melissachua/adv_genomics/output-dir/exon

and got an error message:

FATAL ERROR:TsvFile.cpp:2686: open: Could not open file: '/home/melissachua/adv_genomics/output-dir/celfiles.txt' to read.

Permissions

~/adv_genomics/output-dir$ ls -l
total 153344
-rwxr-xr-x 1 melissachua melissachua 82829219 Jan 29 18:08 HuEx-1_0-st-v2.na24.hg18.probeset_abbr.csv
-rwxr-xr-x 1 melissachua melissachua 12111200 Jan 29 18:04 HuEx-1_0-st-v2.r2.dt1.hg18.full.mps
---x--x--x 1 melissachua melissachua      374 Jan 29 19:01 celfiles.txt
-rwxr-xr-x 1 melissachua melissachua 62068469 Jan 28 11:47 dabg.summary.txt
drwxr-xr-x 2 melissachua melissachua     4096 Jan 29 19:12 exon
drwxr-xr-x 2 melissachua melissachua     4096 Jan 29 19:13 gene

[massa.kassa.sc3na]

From the ls -l it is obvious, that the celfiles.txt does not have the read attribute set (note the missing r). Set it using chmod (usage e.g. here https://wiki.archlinux.org/title/File_permissions_and_attributes)