AWS AMI missing fastqc and related tools

[tejashree1modak]

When I started an EC2 instance based off of the DC AMI as directed in Launching your own AWS instances page, I found out that the image didn't have fastqc or any other related tools installed

ubuntu@ip-172-31-36-97:~/dc_workshop/data/untrimmed_fastq$ fastqc *.fastq*
The program 'fastqc' is currently not installed. You can install it by typing:
sudo apt-get install fastqc
ubuntu@ip-172-31-36-97:~/dc_workshop/data/untrimmed_fastq$ sudo apt-get install fastqc
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
libtcl8.5 libtk8.5 tcl8.5 tk8.5
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
libjbzip2-java libsam-java
Suggested packages:
picard-tools
The following NEW packages will be installed:
fastqc libjbzip2-java libsam-java
0 upgraded, 3 newly installed, 0 to remove and 587 not upgraded.
Need to get 539 kB of archives.
After this operation, 1,264 kB of additional disk space will be used.
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While fixing this in the AMI itself is the ideal solution, in the interim having a documented check in the quality control lesson to ensure fastqc and related tools are installed is very helpful to a new student.

[sstevens2]

Should this issue be closed? The related PR was merged. While I'm not sure it fully addresses the issue, I can report that the last couple times I used the AMI this year it did indeed have all the software installed in it.