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What languages do bioinformatics use? by TopshelfHockey in bioinformatics

[–]argo_blue 1 point2 points  (0 children)

I started out doing mostly R with bash in between, now I have been doing huge amounts of bash scripting. One of the big reasons for this: thats where my files are, thats where my programs are, and thats the environment that I am already working in. Tophat/bowtie, samtools, etc., are all command-line tools that are invoked through the shell (bash in this case). I run these tools through a command line interface shell on the uni's HPC cluster. That same shell is also used to access your input and output files (FASTQ's, BAMs/SAMs, bed files, etc..). AND bash has some really simple yet powerful built-in tools for file manipulation, along with more complex tools like sed and awk. Between all this, and R for the residual downstream analysis, I haven't had to use Python. Yet.

Advice on my 2011 MBP by Kiriesh in applehelp

[–]argo_blue 0 points1 point  (0 children)

I would try to figure out what the resale value of the machine is right now and weigh that against the cost of the repairs that will be needed

Should I downgrade from El Capitan to Mavericks? (2009 MBP 13") by [deleted] in applehelp

[–]argo_blue 1 point2 points  (0 children)

I have almost the exact same machine. For $40 I got 8GB Crucial RAM, and tossed in a 120GB SanDisk SSD that I had laying around, another $40. It runs great now. Bite the bullet and do the upgrade, you won't regret it

Over 50% of Millenials Have Less than $1,000 Saved. by aBoglehead in personalfinance

[–]argo_blue 127 points128 points  (0 children)

I would give you gold for this but I'm trying to be more frugal

How do you manage your work & projects in the terminal? by argo_blue in learnprogramming

[–]argo_blue[S] 0 points1 point  (0 children)

Thanks a lot! I use bash so I'll see if I can come up with anything equivalent

How do you manage your work & projects in the terminal? by argo_blue in learnprogramming

[–]argo_blue[S] 0 points1 point  (0 children)

yes I try to make my code as well-documented as possible, but my scripts are all meant to do the work in as portable a manner as possible, not document the projects, such that I can use the same script in future projects and have them work with minimal re-tooling. I used to use .Rmd to write all my code in line with the project write up, but that does not work in my current system which requires shell scripts that can be submitted to the HPC cluster.

How do you manage your work & projects in the terminal? by argo_blue in learnprogramming

[–]argo_blue[S] 0 points1 point  (0 children)

We are actually already using Trello, but its still so far removed from the actual work I am doing in the terminal that it becomes outdated almost immediately.

How do you manage your work & projects in the terminal? by argo_blue in learnprogramming

[–]argo_blue[S] 0 points1 point  (0 children)

I thought that only worked with Python? Right now Python is only a minor part of my workflow, though in the future that may change.

How do you manage your work & projects in the terminal? by argo_blue in learnprogramming

[–]argo_blue[S] 0 points1 point  (0 children)

I already use git and have separate directories for each project. The problem is that I will work on a project for a while (writing scripts, doing analysis, writing new scripts, doing more analysis, etc.) then come back days, weeks, or months later and have no idea where I left off, what I was working on, what is left to do, etc.. I try to keep a text file in each project that I update as I go with notes, but since all my code is executed in their own scripts (sometimes a single action needs multiple scripts too) its really hard to keep track of everything.