From c49212228e03c72342bca2041b1e91f62fa98984 Mon Sep 17 00:00:00 2001 From: "Kelly Sovacool, PhD" Date: Wed, 23 Oct 2024 15:04:27 -0400 Subject: [PATCH 1/4] fix: update proxy url in setup.md --- docs/HPCDME/setup.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/HPCDME/setup.md b/docs/HPCDME/setup.md index 3b7e3f0..341e8cf 100644 --- a/docs/HPCDME/setup.md +++ b/docs/HPCDME/setup.md @@ -31,9 +31,11 @@ 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 `$USER` with your actual username in the properties file. Bash variables will not be interpolated. +> +> Note: be sure to set the proxy server URL as below (`hpc.server.proxy.url=10.1.200.75`) when running on biowulf/helix. ```bash #HPC DME Server URL @@ -49,7 +51,7 @@ hpc.ssl.keystore.password=changeit #hpc.ssl.keystore.password=hpc-server-store-pwd #Proxy Settings -hpc.server.proxy.url=10.1.200.240 +hpc.server.proxy.url=10.1.200.75 hpc.server.proxy.port=3128 hpc.user=$USER From ecbdc11c96132d59d315431a6e1083a3a07a67ee Mon Sep 17 00:00:00 2001 From: "Kelly Sovacool, PhD" Date: Wed, 30 Oct 2024 15:18:42 -0400 Subject: [PATCH 2/4] docs: don't change changeit everyone agrees it's confusing! --- docs/HPCDME/setup.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/docs/HPCDME/setup.md b/docs/HPCDME/setup.md index 341e8cf..f648698 100644 --- a/docs/HPCDME/setup.md +++ b/docs/HPCDME/setup.md @@ -33,9 +33,11 @@ cp hpcdme.properties-sample hpcdme.properties 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 `$USER` with your actual username in the properties file. Bash variables will not be interpolated. -> -> Note: be sure to set the proxy server URL as below (`hpc.server.proxy.url=10.1.200.75`) when running on biowulf/helix. +**NOTES** + +- Replace `$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 From 9b1e20a7659d9b9130674e5295c7d90fedd261a9 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Wed, 30 Oct 2024 15:26:55 -0400 Subject: [PATCH 3/4] fix: load conda env before running projark --- docs/HPCDME/transfer.md | 44 ++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/docs/HPCDME/transfer.md b/docs/HPCDME/transfer.md index 4b95d18..2066958 100644 --- a/docs/HPCDME/transfer.md +++ b/docs/HPCDME/transfer.md @@ -33,6 +33,28 @@ Rawdata or Project folders from Biowulf can be parked at a secure location after #### 2.1. `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 +``` + +
+ Expected sample output + +```bash +v2.0.2-dev +projark is using the following parkit version: +v2.0.2-dev +``` +
+ ```bash projark --help ``` @@ -72,28 +94,6 @@ 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 -``` - -
- Expected sample output - -```bash -v2.0.2-dev -projark is using the following parkit version: -v2.0.2-dev -``` -
- ##### run `projark` ```bash From 5166c6ead481591cb0134499f14d42e91d6c987a Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Wed, 30 Oct 2024 15:29:09 -0400 Subject: [PATCH 4/4] docs: update static TOC --- docs/HPCDME/transfer.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/HPCDME/transfer.md b/docs/HPCDME/transfer.md index 2066958..e099947 100644 --- 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) @@ -55,6 +56,8 @@ v2.0.2-dev ``` +##### projark help + ```bash projark --help ```