X

README.md

@@ -299,8 +299,8 @@ You can now SSH into the head node with the following command:
 ssh -i /Users/daylily/.ssh/omics-analysis-b.pem [email protected]
 Once logged in, as the 'ubuntu' user, run the following commands:
   cd ~/projects/daylily
-  source dayinit -h
-  source dayinit  --project PROJECT
+  source dyinit -h
+  source dyinit  --project PROJECT
   dy-a local
   dy-r help
  
@@ -493,7 +493,7 @@ bin/daylily-ssh-into-headnode
 **Is `daylily` CLI Available & Working**
 ```bash
 cd ~/projects/daylily
-. dayinit # inisitalizes the daylily cli
+. dyinit # inisitalizes the daylily cli
 dy-a local # activates the local config
 dy-r help # should show the help menu
 ```
@@ -502,7 +502,7 @@ This should produce a magenta `WORKFLOW SUCCESS` message and `RETURN CODE: 0` at
 
 ###### Headnode Confiugration Incomplete
 
-If there is no `~/projects/daylily` directory, or the `dayinit` command is not found, the headnode configuration is incomplete. 
+If there is no `~/projects/daylily` directory, or the `dyinit` command is not found, the headnode configuration is incomplete. 
 
 **Attempt To Complete Headnode Configuration**
 From your remote terminal that you created the cluster with, run the following commands to complete the headnode configuration.
@@ -530,7 +530,7 @@ drwxrwxrwx 3 root root 33K Sep 26 08:35 resources
 ##### Run A Local Test Workflow
 
 ```bash
-. dayinit  --project PROJECT
+. dyinit  --project PROJECT
 dy-a local
 
 head -n 2 .test_data/data/giab_30x_hg38_analysis_manifest.csv
@@ -586,7 +586,7 @@ cd daylily
 
 #  prepare to run the test
 tmux new -s slurm_test
-. dayinit 
+. dyinit 
 dy-a slurm
 
 # create a test manifest for one giab sample only, which will run on the 0.01x test dataset
@@ -642,7 +642,7 @@ cd /fsx/analysis_results/ubuntu/slurm_single
 git clone https://github.com/Daylily-Informatics/daylily.git  # or, if you have set ssh keys with github and intend to make changes:  git clone [email protected]:Daylily-Informatics/daylily.git
 cd daylily
 
-. dayinit  --project PROJECT 
+. dyinit  --project PROJECT 
 dy-a slurm
 
 # TO create a single sample manifest
@@ -665,7 +665,7 @@ cd /fsx/analysis_results/ubuntu/slurm_multi_30x_test
 git clone https://github.com/Daylily-Informatics/daylily.git  # or, if you have set ssh keys with github and intend to make changes:  git clone [email protected]:Daylily-Informatics/daylily.git
 cd daylily
 
-. dayinit  --project PROJECT 
+. dyinit  --project PROJECT 
 dy-a slurm
 
 # copy full 30x giab sample template to config/analysis_manifest.csv
@@ -1007,7 +1007,7 @@ active_aligners:
 ```
 - This will enable running these two tools.  You will also need a liscence file from sentieon in order to run these tools.  
 - Please [contact them](https://www.sentieon.com/company/) to obtain a valid liscense . 
-- Once you have a lisence file, edit the `dayinit` file to include the */fsx/* relative path to this file where `export SENTIEON_LICENSE=` is found.  
+- Once you have a lisence file, edit the `dyinit` file to include the */fsx/* relative path to this file where `export SENTIEON_LICENSE=` is found.  
 - Save the liscence file in the each region specific S3 reference bucket, ie: `s3://PREFIX-omics-analysis-REGION/data/cached_envs/`. When this bucket is mounted to the fsx filesystem, the liscence file will be available to all instances at `/fsx/data/cached_envs/`.
 
 

bin/day_activate

@@ -9,13 +9,13 @@ DP=$DAY_PROJECT
 # Attempt to deactivate any existing environment
 source bin/day_deactivate &> /dev/null 
 echo "Attempting to deactivate existing environments & re-init with --project $DP ."
-. dayinit --project $DP &> /dev/null
+. dyinit --project $DP &> /dev/null
 export DAY_PROFILE=$dayp
 
 echo 
 # Check if DAY_ROOT is set
 if [[ -z "$DAY_ROOT" ]]; then
-    echo "ERROR: DAY_ROOT is not set. Have you executed 'source dayinit'? Use -h for help."
+    echo "ERROR: DAY_ROOT is not set. Have you executed 'source dyinit'? Use -h for help."
     return 2
 fi
 
@@ -74,7 +74,7 @@ if [[ "$pe_ret_code" != "0" ]]; then
     source bin/util/col_error.bash
     echo "ERROR: Activation failed with return code $pe_ret_code."
     echo ""
-    echo "Have you run 'day-build'? If so, try 'bin/day_deactivate reset; source dayinit; day-activate local;'"
+    echo "Have you run 'day-build'? If so, try 'bin/day_deactivate reset; source dyinit; day-activate local;'"
     return $pe_ret_code
 else
     conda activate DAY

bin/day_activate_o

@@ -10,7 +10,7 @@ gold_profiles/$DAY_PROFILE/*"
 fi
 
 if [[ "$1" == "" ]]; then
-    . dayinit
+    . dyinit
 fi
 envi=$1
 
@@ -41,7 +41,7 @@ else
 
     **>> EXPECTED:     $DAY_ROOT
 
-    You are strongly encouraged to run 'day-deactivate', then 'source dayinit && day-activate' from the intended analysis deployment directory.
+    You are strongly encouraged to run 'day-deactivate', then 'source dyinit && day-activate' from the intended analysis deployment directory.
 
     **>> DETECTED:     $PWD
 
@@ -118,7 +118,7 @@ then
     # Something is not right....?
     echo ""
     echo ""
-    echo "DAY_ROOT is not set.  Have you executed 'source dayinit'? Or re-run with -h"
+    echo "DAY_ROOT is not set.  Have you executed 'source dyinit'? Or re-run with -h"
     ret_code=2
 
     if [[ "$1" == "h" || "$1" == "-h" || "$1" == "--help" || "$1" == "help" ]]; then
@@ -180,7 +180,7 @@ if [[ "$c" == "" ]]; then
         echo "    SUCCESS!   But you seem to be missing the pkg colr, just attempted to add it."
     else
         echo " ---==]]>>>>> ERROR !!!!!!!!!!! "
-        echo " Returned with code $ex_code, try running a test 'day-activate local; day-run  -c 3 -j 2 sleep ' otherwise day-deactivate; bash; source dayinit; day-activate local;   If you have a 'colr not found error, pip may not have completed sucessfully, try:  'conda activate DAY; pip install --no-input -i https://pypi.org/simple --extra-index-url https://pypi.org/simple  chromedriver-binary-auto   rgbw-colorspace-converter  colr docopt snakemake pandas xmltodict wrapt
+        echo " Returned with code $ex_code, try running a test 'day-activate local; day-run  -c 3 -j 2 sleep ' otherwise day-deactivate; bash; source dyinit; day-activate local;   If you have a 'colr not found error, pip may not have completed sucessfully, try:  'conda activate DAY; pip install --no-input -i https://pypi.org/simple --extra-index-url https://pypi.org/simple  chromedriver-binary-auto   rgbw-colorspace-converter  colr docopt snakemake pandas xmltodict wrapt
           "
         return 22
     fi
@@ -207,7 +207,7 @@ if [[ "$ret_code" != "0" ]]; then
     colr "|       ! \ " "turquoise" "debianred" "f"
     colr "|_________/  " "turquoise" "debianred" "f"
     colr "Something went awry. Check the README for alternate install instructuions. Else, ping JEM. ret code was $ret_code" "orangered" "black" "b"
-    echo "Have you run day_build?  If so this is worth a shot:'bin/day_deactivate reset; source dayinit; day-activate local;'"
+    echo "Have you run day_build?  If so this is worth a shot:'bin/day_deactivate reset; source dyinit; day-activate local;'"
     return 0
 else
    colr "       _______ GREAT SUCCESS _______       " "$DY_IT0" "$DY_IB0" "$DY_IS1"

bin/day_build

@@ -1,9 +1,9 @@
 #!/usr/bin/env bash
 # This script is intended to be sourced, not executed directly.
 
-# Check if DAY_ROOT is set; if not, source dayinit
+# Check if DAY_ROOT is set; if not, source dyinit
 if [[ -z "$DAY_ROOT" ]]; then
-    source dayinit
+    source dyinit
 fi
 
 envi="$1"
@@ -33,8 +33,8 @@ else
     fi
 fi
 
-# Source dayinit for local setup
-source dayinit local &> /dev/null
+# Source dyinit for local setup
+source dyinit local &> /dev/null
 
 # Check if 'colr' command is available
 if ! command -v colr &> /dev/null; then
@@ -59,10 +59,10 @@ else
     else
         echo "GREAT SUCCESS!"
         export PS1="$DYPS1 $PS1"
-        source dayinit local &> /dev/null
+        source dyinit local &> /dev/null
         echo "Please start a new bash session and test the install:"
         echo "  bash;"
-        echo "  source dayinit;"
+        echo "  source dyinit;"
         echo "  dy-a local"
         echo "  dy-r help"
     fi

bin/day_build_o

@@ -1,7 +1,7 @@
 #!/bin/echo "this script is intended to only be sourced"
 
 if  [[ "$DAY_ROOT" == "" ]]; then
-    . dayinit
+    . dyinit
 fi
 
 envi=$1
@@ -58,7 +58,7 @@ fi
 
 
 
-source dayinit local > /dev/null 2>&1
+source dyinit local > /dev/null 2>&1
 
 c=`which colr` &> /dev/null || ls &> /dev/null
 
@@ -96,11 +96,11 @@ else
   else
     colr "       _______ GREAT SUCCESS _______       " "chartreuse" "darkgreen" "b"
     export PS1="$DYPS1 $PS1"
-    source dayinit local > /dev/null 2>&1
+    source dyinit local > /dev/null 2>&1
     colr "       please start a new bash session and test the install:
 
         bash ;
-        source dayinit;
+        source dyinit;
         dy-a local
 	dy-r help
 	"	

bin/day_deactivate

@@ -15,7 +15,7 @@ usage() {
     echo "Usage: day-deactivate [activate|reset|--help]"
     echo ""
     echo "This script deactivates the Daylily environment by:"
-    echo "  - Clearing the DAY_ROOT, DAY_PROFILE, and DAY_BIOME and other dayinit set environment variables."
+    echo "  - Clearing the DAY_ROOT, DAY_PROFILE, and DAY_BIOME and other dyinit set environment variables."
     echo "  - Attempting to deactivate any active DAY conda environments."
     echo "  - Restoring the original PATH and PS1 if they were modified."
     echo "  - Unaliasing Daylily CLI commands."

bin/day_deactivate_o

@@ -26,7 +26,7 @@ fi
 
 ret_msg=""
 if [[ $DAY_ROOT == "" && $DAY_PROFILE == "" ]]; then
-    ret_msg="No DAY environment was detected as active.  However, if this is in error, try:  'source dayinit; day-deactivate reset;'"
+    ret_msg="No DAY environment was detected as active.  However, if this is in error, try:  'source dyinit; day-deactivate reset;'"
 fi
 
 if [[ $1 == "activate" ]]; then
@@ -66,7 +66,7 @@ fi
 echo " "
 echo ' '
 
-echo " ... if deactivate only partially ran and left a weird shell prompt, try: 'source dayinit; day-deactivate reset;' "
+echo " ... if deactivate only partially ran and left a weird shell prompt, try: 'source dyinit; day-deactivate reset;' "
 
 return 0
 

bin/daylily-cfg-headnode

@@ -107,18 +107,18 @@ ssh -i "$pem_file" ubuntu@"$cluster_ip_address"  -o StrictHostKeyChecking=no   -
 # Initialize and configure the Daylily environment on the head node
 echo "Configuring Daylily environment on the head node..."
 ssh -t -i "$pem_file" ubuntu@"$cluster_ip_address"  -o StrictHostKeyChecking=no   -o UserKnownHostsFile=/dev/null \
-    "sudo su - $duser -c 'cd ~/projects/daylily && source dayinit --skip-project-check  && source bin/day_build'"
+    "sudo su - $duser -c 'cd ~/projects/daylily && source dyinit --skip-project-check  && source bin/day_build'"
 
 # Run a simple help test for Daylily remotely
 echo "Running a simple help test on the head node..."
 ssh -t -i "$pem_file" ubuntu@"$cluster_ip_address"  -o StrictHostKeyChecking=no   -o UserKnownHostsFile=/dev/null \
-    "sudo su - $duser -c 'cd ~/projects/daylily && source dayinit --skip-project-check  && source bin/day_activate local && source bin/day_run help'"
+    "sudo su - $duser -c 'cd ~/projects/daylily && source dyinit --skip-project-check  && source bin/day_activate local && source bin/day_run help'"
 
 
 # start building the minimal cached envs
 echo "Building the minimal cached environments ..."
 ssh -t -i "$pem_file" ubuntu@"$cluster_ip_address"  -o StrictHostKeyChecking=no   -o UserKnownHostsFile=/dev/null \
-    "sudo su - $duser -c 'cd ~/projects/daylily && source dayinit --skip-project-check  && source bin/day_activate local && source bin/day_run --conda-create-envs-only produce_snv_concordances produce_tiddit  '"
+    "sudo su - $duser -c 'cd ~/projects/daylily && source dyinit --skip-project-check  && source bin/day_activate local && source bin/day_run --conda-create-envs-only produce_snv_concordances produce_tiddit  '"
 
 
 
@@ -127,7 +127,7 @@ echo "You can now SSH into the head node with the following command:"
 echo "ssh -i $pem_file ubuntu@$cluster_ip_address"
 echo "Once logged in, as the 'ubuntu' user, run the following commands:"
 echo "  cd ~/projects/daylily"
-echo "  source dayinit " 
+echo "  source dyinit " 
 echo "  dy-a local"
 echo "  dy-r help"
 echo " "

config/day/day_env_installer.sh

@@ -107,7 +107,7 @@ else
         echo "DAY environment created successfully."
         echo ""
         echo "Try the following commands to get started:"
-        echo "  source dayinit --project <PROJECT>"
+        echo "  source dyinit --project <PROJECT>"
         echo "  dy-a local"
         echo "  dy-r help"
     else
@@ -119,7 +119,7 @@ fi
 echo ""
 echo "Installation complete."
 echo "Please log out and log back in, then run:"
-echo "  source dayinit --project <PROJECT>"
+echo "  source dyinit --project <PROJECT>"
 echo "  dy-a local"
 echo "  dy-r help"
 

config/day/day_env_installer.sh_o

@@ -99,7 +99,7 @@ conda config --add channels bioconda
 
 mgcnt=$(ls -d1 "$(dirname $(which conda))"/../envs/DAY | wc -l)
 if [[ "$mgcnt" == "0" ]]; then
-    echo "Installing DAY \(which will be sourced for you when you \'source dayinit  --project <PROJECT> \' \(see docs\)  you should not need to source MG directly.  Beginning install... "
+    echo "Installing DAY \(which will be sourced for you when you \'source dyinit  --project <PROJECT> \' \(see docs\)  you should not need to source MG directly.  Beginning install... "
     echo "..."
     sleep 1.4
 
@@ -108,7 +108,7 @@ if [[ "$mgcnt" == "0" ]]; then
     echo "Install exited with > $? < (if not zero, not the best sign)."
     echo "try the following:
 
-       source dayinit  --project <PROJECT> ; dy-a local; dy-r help;
+       source dyinit  --project <PROJECT> ; dy-a local; dy-r help;
 
        #initialized the day CLI, activate the local env settings, runs day to get basic help info on targets
        "
@@ -127,6 +127,6 @@ fi;
 
 echo "==="
 echo "___"
-echo 'you should log out of this shell and log back into a fresh shell, run source dayinit  --project <PROJECT> , dy-a *****, etc.'
+echo 'you should log out of this shell and log back into a fresh shell, run source dyinit  --project <PROJECT> , dy-a *****, etc.'
 
 return 0

config/day/env.sh

@@ -2,7 +2,7 @@
 #conda_bin=$(which conda)
 #conda_dir=$(dirname $conda_bin)
 #if [[ $conda_dir == "" ]]; then
-#    echo" >>> ERROR: conda has not been found in your PATH.  If you do not have conda installed, you may run the mod installer+build command: source dayinit  --project <PROJECT> && mod-activate BUILD_all"
+#    echo" >>> ERROR: conda has not been found in your PATH.  If you do not have conda installed, you may run the mod installer+build command: source dyinit  --project <PROJECT> && mod-activate BUILD_all"
 #fi
 
 

config/day/env.sh_o

@@ -2,7 +2,7 @@ conda activate || echo NOCONDA
 conda_bin=$(which conda)
 conda_dir=$(dirname $conda_bin)
 if [[ $conda_dir == "" ]]; then
-    echo" >>> ERROR: conda has not been found in your PATH.  If you do not have conda installed, you may run the mod installer+build command: source dayinit  --project <PROJECT> && mod-activate BUILD_all"
+    echo" >>> ERROR: conda has not been found in your PATH.  If you do not have conda installed, you may run the mod installer+build command: source dyinit  --project <PROJECT> && mod-activate BUILD_all"
 fi
 
 

config/day_examples/vanilla_analysis_manifest/README.md

@@ -101,7 +101,7 @@ Rclone is a very feature rich tool.  You can find the docs here.  In addition to
 
 ```
 cd $DAY_ROOT
-source dayinit  --project <PROJECT>
+source dyinit  --project <PROJECT>
 mg-a local
 rclone -L --config config/day_example_analysis_manifests/rclone_xxx_local_example.conf cat localxxx:/fsx/data/external_data/research_experiments/ManualRuns/EX3636/b37/wgs_data/SQ42092_LS1585266_RE2698_G3/Lib_for_SequenceIndex_SQ42092.aligned.deduped.sort.bam | samtools view -H
 ```

docs/first_ephemeral_cluster_analysis.md

@@ -49,7 +49,7 @@ cd daylily
 cp .test/
 
 # initialize the DAY conda env + other helpful tools
-. dayinit  # you can speciy --project AWSBUDGETNAME to change from the default region specific budget. New budgets created in AWS must also be added to the allowed ubuntu projects in /opt/slurm/etc/projects_list.conf to be recognized by the cluster. jobs will not launch if the budget is not recognized.
+. dyinit  # you can speciy --project AWSBUDGETNAME to change from the default region specific budget. New budgets created in AWS must also be added to the allowed ubuntu projects in /opt/slurm/etc/projects_list.conf to be recognized by the cluster. jobs will not launch if the budget is not recognized.
 
 # move an analysis manifest into place, which haas a tiny toy dataset.
 cp .test_data/data/0.01xwgs_HG002_hg38.samplesheet.csv confiig/analysis_manifest.csv # YOU WILL USE THE ./bin/create_analysis_manifest script to create your own manifest for your own data when the time comes.
@@ -110,7 +110,7 @@ ls results/day/{hg38,b37}/reports/*.html
 Copy the pre-configured giab analysis manifest for hg38, and run the analysis. This manifest points to the fastq.gz files for each, as well as the truth data set needed to produce the concordance reports.
 ```bash
 
-. dayinit 
+. dyinit 
 dy-a slurm
 
 vi config/day_profiles/slurm/rule_config.yaml # the default build is hg38, so no changes are needed here 
@@ -130,7 +130,7 @@ ls results/day/hg38/other_reports/*giab*
 You will need to modify the rule_config.yaml to use b37, and copy the pre-configured giab analysis manifest for b37.
 ```bash
 
-. dayinit 
+. dyinit 
 dy-a slurm
 
 # you will need to chang ethe reference build to b37 from hg38
@@ -183,7 +183,7 @@ bash bin/create_analysis_manifest -f fastq_manifest.tsv -o config/analysis_manif
 - From the github repo directory on the headnode, in a tmux terminal, with your desired `config/analysis_manifest.csv` in place:
 ```bash
 
-. dayinit
+. dyinit
 dy-a slurm
 
 # If you wish to enable an aligner other than bwa mem2 or a variant caller other than deep variant, you will need to edit the config/day_profiles/slurm/rule_config.yaml before proceeding.  
@@ -208,7 +208,7 @@ find results/ | grep -E 't.vcf.gz|bam.bai'
 - From the github repo directory on the headnode, in a tmux terminal, with your desired `config/analysis_manifest.csv` in place:
 ```bash
 
-. dayinit
+. dyinit
 dy-a slurm
 
 dy-r produce_multiqc_final_wgs -p -k -j 9 -n

docs/ops/dycli.md

@@ -4,8 +4,8 @@
 ```bash
 
 # init the dy-cli
-source dayinit -h
-source dayinit  --project <PROJECT>
+source dyinit -h
+source dyinit  --project <PROJECT>
 
 # activate the local or slurm running environment
 dy-a local # or slurm  # tab complete for avail envs