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update for 2024

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Natalie Elphick 2024-03-04 13:06:38 -08:00
parent ce523c9b45
commit 26321dd914
6 changed files with 12780 additions and 682 deletions
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6688
docs/Intro_to_Unix_Part_1.html
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docs/Intro_to_Unix_Part_2.html
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34
intro-unix-command-line/Intro_to_Unix_Part_1.Rmd
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@ -1,7 +1,7 @@
---
title: "Introduction to Unix Command-line - Part 1"
author: "Natalie Elphick"
date: "April 17th"
date: "March 11th 2024"
knit: (function(input, ...) {
rmarkdown::render(
input,
@ -15,7 +15,7 @@ output:
```{r, setup, include=FALSE}
knitr::opts_knit$set(root.dir = './unix_workshop_2023')
knitr::opts_knit$set(root.dir = './unix_workshop_2024')
```
@ -87,17 +87,17 @@ cd unix_workshop
```{r, engine='bash', eval=FALSE, results="hide", highlight=FALSE, comment=NA, echo = TRUE}
curl -L -o unix_workshop_2023.tar.gz 'https://www.dropbox.com/s/smb12au2y82jmvq/unix_workshop_2023.tar.gz?dl=0'
curl -L -o unix_workshop_2024.tar.gz 'https://www.dropbox.com/scl/fi/o8msrl3a1k986jvjll4mv/unix_workshop_2024.tar.gz?rlkey=m7jfkvpz0iq12zdzphq7013l5&dl=0'
```
```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA, echo = TRUE}
tar -xzf unix_workshop_2023.tar.gz
tar -xzf unix_workshop_2024.tar.gz
```
```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA, echo = TRUE}
cd unix_workshop_2023
cd unix_workshop_2024
```
@ -227,7 +227,7 @@ pwd
```
```{r, engine='bash', eval=TRUE, results='markup', highlight=FALSE, comment=NA, echo=FALSE}
echo "/Users/your_username/unix_workshop_2023"
echo "/Users/your_username/unix_workshop_2024"
```
- The default working directory when you log in or open a terminal is your user home directory <span style="background-color:#242423; color:white">&nbsp;~&nbsp; </span>
@ -256,7 +256,7 @@ ls -lah part_1
## cd: move to a directory
```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA}
cd unix_workshop_2023/part_1
cd unix_workshop_2024/part_1
ls -l
```
@ -575,23 +575,21 @@ https://www.surveymonkey.com/r/DY7K5ZY
## Upcoming Data Science Training Program Workshops
[Linear Mixed Effects Modeling](https://gladstone.org/index.php/events/linear-mixed-effects-modeling-0)
April 24-April 25, 2023 10:00am-12:00pm PDT
[Machine Learning](https://gladstone.org/index.php/events/machine-learning)
April 28, 2023 10:00am-12:00pm PDT
[Advanced Cytoscape Automation](https://gladstone.org/index.php/events/advanced-cytoscape-automation-2)
May 2, 2023 1:00-4:00pm PDT
[Introduction to RNA-Seq Analysis](https://gladstone.org/index.php/events/introduction-rna-seq-analysis-4)
May 15-May 16, 2023 9:00am-12:00pm PDT
[Introduction to Pathway Analysis](https://gladstone.org/events/introduction-pathway-analysis-1)
April 2, 2024 1:00-4:00pm PDT
[Statistics of Enrichment Analysis Methods](https://gladstone.org/events/statistics-enrichment-analysis-methods-0)
April 11-April 12, 2024 1:00-3:00pm PDT
[Working on Wynton](https://gladstone.org/events/working-wynton)
April 15, 2024 1:00-4:00pm PDT
[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models)
April 25-April 26, 2024 1:00-3:00pm PDT
[Complete Schedule](https://gladstone.org/events?series=data-science-training-program)

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intro-unix-command-line/Intro_to_Unix_Part_2.Rmd
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@ -1,7 +1,7 @@
---
title: "Introduction to Unix Command-line - Part 2"
author: "Natalie Elphick"
date: "April 18th"
date: "March 12th 2024"
knit: (function(input, ...) {
rmarkdown::render(
input,
@ -13,7 +13,7 @@ output:
css: style.css
---
```{r, setup, include=FALSE}
knitr::opts_knit$set(root.dir = './unix_workshop_2023')
knitr::opts_knit$set(root.dir = './unix_workshop_2024')
```
##
@ -50,21 +50,21 @@ cd unix_workshop
```{r, engine='bash', eval=FALSE, results="hide", highlight=FALSE, comment=NA, echo = TRUE}
curl -L -o unix_workshop_2023.tar.gz 'https://www.dropbox.com/s/smb12au2y82jmvq/unix_workshop_2023.tar.gz?dl=0'
curl -L -o unix_workshop_2024.tar.gz 'https://www.dropbox.com/s/smb12au2y82jmvq/unix_workshop_2024.tar.gz?dl=0'
```
```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA, echo = TRUE}
tar -xzf unix_workshop_2023.tar.gz
tar -xzf unix_workshop_2024.tar.gz
```
```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA, echo = TRUE}
cd unix_workshop_2023
cd unix_workshop_2024
```
```{r, engine='bash', eval=TRUE, results="hide", highlight=FALSE, comment=NA, echo = TRUE}
curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.109.refseq.tsv.gz
curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.111.refseq.tsv.gz
```
# File Compression
@ -414,17 +414,21 @@ https://www.surveymonkey.com/r/DY7K5ZY
## Upcoming Data Science Training Program Workshops
[Linear Mixed Effects Modeling](https://gladstone.org/index.php/events/linear-mixed-effects-modeling-0)
April 24-April 25, 2023 10:00am-12:00pm PDT
[Introduction to Pathway Analysis](https://gladstone.org/events/introduction-pathway-analysis-1)
April 2, 2024 1:00-4:00pm PDT
[Machine Learning](https://gladstone.org/index.php/events/machine-learning)
April 28, 2023 10:00am-12:00pm PDT
[Statistics of Enrichment Analysis Methods](https://gladstone.org/events/statistics-enrichment-analysis-methods-0)
April 11-April 12, 2024 1:00-3:00pm PDT
[Advanced Cytoscape Automation](https://gladstone.org/index.php/events/advanced-cytoscape-automation-2)
May 2, 2023 1:00-4:00pm PDT
[Working on Wynton](https://gladstone.org/events/working-wynton)
April 15, 2024 1:00-4:00pm PDT
[Introduction to RNA-Seq Analysis](https://gladstone.org/index.php/events/introduction-rna-seq-analysis-4)
May 15-May 16, 2023 9:00am-12:00pm PDT
[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models)
April 25-April 26, 2024 1:00-3:00pm PDT
[Complete Schedule](https://gladstone.org/events?series=data-science-training-program)

0
intro-unix-command-line/unix_workshop_2023/part_1/.hidden_file.txt → intro-unix-command-line/unix_workshop_2024/part_1/.hidden_file.txt
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intro-unix-command-line/unix_workshop_2023/part_1/list_numbers.tsv → intro-unix-command-line/unix_workshop_2024/part_1/list_numbers.tsv
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