Merge pull request #12 from CCBR/iss-10

improve HPCDME instructions
CCBR · Oct 30, 2024 · 21065b5 · 21065b5
2 parents 16535b0 + 5166c6e
commit 21065b5
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diff --git a/docs/HPCDME/setup.md b/docs/HPCDME/setup.md
@@ -31,9 +31,13 @@ cp hpcdme.properties-sample hpcdme.properties
 
 #### Customize properties file
 
-Some of the parameters in this file have become obsolete over the course of time and are commmented out. Change paths and default values, as needed
+Some of the parameters in this file have become obsolete over the course of time and are commmented out. Change paths and default values, as needed.
 
-> Note: replace `$USER` with your actual username in the properties file. Bash variables will not be interpolated.
+**NOTES**
+
+- Replace `$USER` with your actual username in the properties file. Bash variables will not be interpolated.
+- Leave `hpc.ssl.keystore.password=changeit` as-is. `changeit` is not a variable but the actual password for our team.
+- Be sure to set the proxy server URL as below (`hpc.server.proxy.url=10.1.200.75`) when running on biowulf/helix.
 
 ```bash
 #HPC DME Server URL
@@ -49,7 +53,7 @@ hpc.ssl.keystore.password=changeit
 #hpc.ssl.keystore.password=hpc-server-store-pwd
 
 #Proxy Settings
-hpc.server.proxy.url=10.1.200.240
+hpc.server.proxy.url=10.1.200.75
 hpc.server.proxy.port=3128
 
 hpc.user=$USER

diff --git a/docs/HPCDME/transfer.md b/docs/HPCDME/transfer.md
@@ -3,9 +3,10 @@
 - [1. Background](#1-background)
 - [2. parkit](#2-parkit)
   - [2.1. `projark` usage](#21-projark-usage)
+    - [load conda env](#load-conda-env)
+    - [`projark` help](#projark-help)
   - [2.2. `projark` testing](#22-projark-testing)
     - [get dummy data](#get-dummy-data)
-    - [load conda env](#load-conda-env)
     - [run `projark`](#run-projark)
     - [verify transfer](#verify-transfer)
     - [cleanup](#cleanup)
@@ -33,6 +34,30 @@ Rawdata or Project folders from Biowulf can be parked at a secure location after
 
 ####  2.1. <a name='projarkusage'></a>`projark` usage
 
+##### load conda env
+
+```bash
+# source conda
+. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
+# activate parkit or parkit_dev environment
+conda activate parkit
+# check version of parkit
+parkit --version
+projark --version
+```
+
+<details>
+  <summary><em>Expected sample output</em></summary>
+
+```bash
+v2.0.2-dev
+projark is using the following parkit version:
+v2.0.2-dev
+```
+</details>
+
+##### projark help
+
 ```bash
 projark --help
 ```
@@ -72,28 +97,6 @@ cp -r /data/CCBR/projects/CCBR-12345 /data/$USER/parkit_tmp/CCBR-12345-$USER
 echo $HPC_DM_UTILS
 ```
 
-##### load conda env
-
-```bash
-# source conda
-. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
-# activate parkit or parkit_dev environment
-conda activate parkit
-# check version of parkit
-parkit --version
-projark --version
-```
-
-<details>
-  <summary><em>Expected sample output</em></summary>
-
-```bash
-v2.0.2-dev
-projark is using the following parkit version:
-v2.0.2-dev
-```
-</details>
-
 ##### run `projark`
 
 ```bash