There are 2 files.  
One to prepare and the second one to modify.
You prepare those 2 files on your PC.

First file is "_ids.txt"
--------------------------
Example:

ATF2 
FOS 
JUN 
MAPK1 
MAPK10 
MAPK11 
MAPK14 
MAPK3 
MAPK8 
MAPK9

Note 1: IDs either all Uniprot or Gene symbol or Egid.
Note 2: The formatting is as one ID per line. In other words; with a new 
line as delimiter.

Second file is "_config.txt" (You can use it as template to modify)
-------------------------------------------------------------------------------
Example:

# IDs Type Choice
# - Uncomment the only one of those five:
# Uniprot ID
Gene Symbol
# Egid


# Exclude pathways where only one ID from the input list was found.
# - Uncomment the only one of those five:
Yes
# No


# Data component
# - Uncomment the only one of those five:
Literature curated (core) pathway memberships
# Extended pathway associations. Protein interaction set: Experimentally detected PPIsMinimum confidence level for predicted associations: 0.99
# Extended pathway associations. Protein interaction set: Experimentally detected and computationally predicted PPIs (full IID)Minimum confidence level for predicted associations: 0.99


# Data sources
# - Use some or all of those:
#   ACSN2,BioCarta,HumanCyc,KEGG,Panther_Pathway,PathBank,PharmGKB,REACTOME,MetabolicAtlas,SIGNOR 3.0,UniProt_Pathways,WikiPathways
# - Comma delimited.
# - Mind exact spelling.
ACSN2,BioCarta,HumanCyc,KEGG,Panther_Pathway,PathBank,PharmGKB,REACTOME,MetabolicAtlas,SIGNOR 3.0,UniProt_Pathways,WikiPathways


# Pathway types
# - Use some or all of those:
#   Cellular processes and organization,Diseases,Drugs and vitamins,Environmental information processing,Genetic information processing,Metabolism,Organismal systems
# - Comma delimited.
# - Mind exact spelling.
Cellular processes and organization,Diseases,Drugs and vitamins,Environmental information processing,Genetic information processing,Metabolism,Organismal systems


# Deploy 'q-value (FDR: BH-method)' to cut off the insignificant results 
# Use the only one of the follow settings   
# 0.01  
0.05
# 0.1  
# All  


        

<1> PuTTY
- ssh to nn.nn.n.85
- cd __pathDIA
- ls                                          ### you will see a set of files
        

<2> WinSCP
- winscp to nn.nn.nn.85
- double click on the yellow square at the left of __pathDIA
- (you will see) the same files that you see in PuTTY


<3> Don't change anything. Let's try samples.
- (type) run_small.sh (press  on your keyboard)
- (for this my sample, in 5-6 seconds, you will see) 
        

<4>
- switch to WinSCP.
- (find and click) refresh green button above the right panel
- you will see 
        

- bring "pathDIA_SearchGenes_2024_nn_nn_nn_nn_nn.txt" file to your computer. This is the results file.

Note: Use "run_small.sh" when you have time to keep the PuTTY window open and wait for results.


<5> If you expect that sample will run long and you need to close the PuTTY window then:
- (type) run_big.sh 
- you will see
        

- (now you can type) exit  (to close PuTTY window. Your job will continue to run without the PuTTY window.)

- from now you need to periodically fire WinSCP and connect to Server 85 to see whether the job is already finished.
- (when you see) pathDIA_SearchGenes_2024_nn_nn_nn_nn_nn.txt file (then the results are already here). 
- (notice also) log.txt file which contents the time when the job was started. (the top lines)
- pathDIA_SearchGenes_2024_nn_nn_nn_nn_nn.txt contents the time when the job was finished (the top lines)

Note: ALWAYS remember to USE EXACT SPELLING as provided in the "_config.txt" file