Installing Stacks on a RedHat Distro

So, you have realized the value of the program Stacks (Catchen et al., 2011) and you want to install it. But you’ve be forewarned that the installation process will turn your hair white as the installation guide is written for Debian distros and you run RedHat/ Fedora. Here is a Debian to RedHat translation of the Stacks Installation Guide, including painfully detailed sections on things you probably already know. I cant promise it is perfect, but it worked.

Prerequisites

Stacks requires a lot of dependencies to run and installing them properly is important. So, read their installation guide well.

You probably want to do the following as a root user:

% sudo -s

1. First you install mysql, php & apache (httpd):

  % yum install mysql-server php httpd

2. Then you install php & mysql extensions:

  % yum install php-pear-mdb2 php-pear-mdb2-driver-mysql

3. Install a driver that helps perl interface with mysql (libdbd-mysql-perl in guide):

  % yum install perl-DBD-MySQL

Sometimes this gets installed as a dependency when you instal mysql-server

4. Install Samtools:

  % yum install samtools

5. Install a package that deals with SAM and BAM files (libbam-dev in guide):

  % yum install samtools-devel

Building Stacks 

This actually works with the script provided by Stacks. Before you do this you need to download the tarball from their website.

% tar xfvz stacks_x.xx.tar.gz
% cd stacks_x.xx
% ./configure
% make

% make install

Configuring MySQL

Start mySQL.

% service mysqld start
% cd /usr/local/share/stacks/sql/
% cp mysql.cnf.dist mysql.cnf

Add a user to mysql for stacks

% mysql > CREATE USER 'stacks_user'@'localhost' IDENTIFIED BY 'stackspassword';

Where stacks_user is whatever username you want and stackspassword is the password of your choice.

Give your mysql user access to all databases:

% mysql> GRANT ALL ON *.* TO 'stacks_user'@'localhost' IDENTIFIED BY 'stackspassword';

Now the protocol says “Edit /usr/local/share/stacks/sql/mysql.cnf to contain the username and password you specified to MySQL”. To do this in the shell you have to use the Vi. Incase you’ve never used it before, I listed the steps below.

First open mysql.cnf

% vi /usr/local/share/stacks/sql/mysql.cnf

Hitting ‘i’ will put vi into insert or edit mode. Edit the username = stacks_user and password = stackspassword. Hit ctrl + c to exit insert mode.

To save the document and quite vi enter ‘:’. This puts vi in command mode. Then type ‘ w q’ and hit [enter]. Your document has been edited and saved.

For more details on vi: Scroll to 7.2.1. Shell Prompt Text Editors.

Enabling the Stacks Web Interface 

So, they want to to create a stacks.conf file in the httpd.conf directory.

% vi /etc/httpd/conf/stacks.conf

Paste the following text into your new file:

<Directory “/usr/local/share/stacks/php”>
Order deny,allow
Deny from all
Allow from all
</Directory>

Alias /stacks “/usr/local/share/stacks/php”

Ctrl + C –> exit insert mode.

: w q [enter] –>  save and quit.

Restart the apache server:

% /sbin/service httpd restart

Now, you need to edit the php config file to include your mysql username and password.

% cp /usr/local/share/stacks/php/constants.php.dist /usr/local/share/stacks/php/constants.php

% vi /usr/local/share/stacks/php/constants.php

i –> insert mode. Enter your mysql user name and password.

Ctrl + c

w q [enter]

Enabling web-based exporting from MySQL database

% chown www /usr/local/share/stacks/php/export

Where ‘www’ is your web server username. If you don’t know what your username is try the whoami command.

Congratulations! You’ve installed stacks!

Why I love The Mindy Project

There has been a news story circling around about Mindy Kaling, regarding the diversity on her show. When asked about the lack of diversity on her show at a panel she responded with, “I’m a fucking Indian woman who has her own fucking network television show, OK?” I can understand her frustration: everyone expects that she, as a woman of color should make her show the most melting pot-diverse-equality filled production of all time.  While  I can see the perspective that comes with this sentiment, I am skeptical regarding its merit. These critics have cited Shonda Rhimes as someone that Mindy Kaling should aspire to be like – utilizing blind casting and having comparably diverse casts. I do support Shonda Rhimes choices, and believe that her usage of blind casting is extremely beneficial to the TV industry. However, there is a major distinction that exists between shows like Grey’s Anatomy and The Mindy Project; and in this distinction lies the strength of the latter.

the-mindy-project

Grey’s Anatomy is essentially a soap opera – I take no issue with that, but it is true. I actually, as a guilty pleasure, watch it often. I must, however, note that while numerous things happen throughout the show’s timeline it presents a remarkable stagnation whereby one can miss seasons at a time and not feel the slightest bit lost. Crisis after crisis befall the characters and yet nothing really changes in the long run; such is the character of a soap opera. You are meant to get roped into their world where you are more likely to be in a plane crash, get shot, drown, get electrocuted, etc. than to experience any long-lived sociopolitical struggles. Grey’s Anatomy is an escape where ethnicity of the characters matters little to the greater story line or show, allowing blind casting to be a possibility. This isn’t a bad thing, shows like this are important to the growth of diversity in the media.

The Mindy Project, to me, represents a different kind of television when compared to Grey’s. Mindy Lahiri, the protagonist, is a brilliant OB/GYN who is a partner at a primarily white male dominated practice in New York city. While this show could pretend that women and people of color are well represented in the high paying job market and blindly cast the actors, it does not – and with good reason. The show, while often ridiculous and dramatic, tackles an important topic: the experiences of a woman of color in a position of authority in a predominately white and male workplace. To me representing this in the media is equally important as putting up a diverse front. I am in a field in which women and people of color show low representation as you go up the food chain. It is nice to have a show that I can identify with, without being caught in some sort of fantasy world.

Why changing your skin color for Halloween is insensitive

The news has been saturated with terrible people doing terrible things for Halloween as of late. Many of them made the very poor decision of donning blackface as part of their costume. As pictures of these costumes reached the internet, most people were horrified and outraged – and rightfully so. Others, however, defended them saying ‘its just a costume’ or ‘they were emulating a the culture or a [insert race] celebrity – it is flattery!’ I do understand that these costumes can be put in different categories.

There are these guys who decided to mock the murder of a kid and on top of that in blackface! I personally hope their stupidity eventually brings about their demise.

Then there are these girls who actually decided to be a race for Halloween! I cannot even imagine what was going through their heads when they decided to do this. It probably involved something like ‘*racism* LOL *racism* JK *racism*’.  This falls under the category that includes the people who dress up as ‘Indians’ and ‘Mexicans’ – except these girls went in blackface!!! Cultural appropriation is a whole other discussion which will be left for another day.

image

And finally, there are the people who wanted to be their favorite celebrity for Halloween. Like this guy who wanted to be Lil Wayne and decided to achieve his goal in blackface.

image

The last category brings in the most support for people who don blackface. Many argue that it is a form of flattery or that they weren’t being malicious like the ones above. And while I do agree that some of these people may just be ignorant and not mini-devils on the earthly plane, this is still very offensive! First, there is the historical aspect, which I don’t feel like I need to explain. Second, and this applies to blackface and brownface alike, the need to change your skin color to portray a celebrity or character suggests that you define this person within their race. And that is the most unkindest cut of all.

The people who do this are basically suggesting that no matter how famous you get or how much you change the world in the end you are seen only within the boundaries of your race. When people decide to dress up as Britney Spears for Halloween they think of the outfits, the hair, etc. and not the fact that she is white. But when an actor/ musician is of color all of a sudden it seems pertinent to change one’s skin color. Does the man above really think that its Lil Wayne’s skin color that defines the image he has probably spent thousands of dollars developing? I hardly think that is logical. And neither is restricting someone’s identity to the confines of their race.

A response to ‘Don’t be that dude: Handy tips for the male academic’ and comments surrounding it

A recent blog post from ‘Tenure, She Wrote’  titled “Don’t be that dude: Handy tips for the male academic” has been making its rounds around the interwebs. I contributed to this by tweeting about it, which actually is what led me to write this post. A friend of mine and fellow grad student replied to my tweet citing some issues she had with the article. This led me consider the merits and drawbacks of some of the points raised in this post in more detail. You can (by that I mean should) read the post here: Don’t be that dude.

The article addresses 20 different ways through which men in academics can aid in providing a platform for gender equity. I will only address the points that I or members of the blogosphere find contentious.

2. Don’t comment on a woman’s appearance in a professional context. It doesn’t matter what your intentions are; it’s irrelevant. 

I think this is a little extreme. I agree there is a lot of prejudice and pressure surrounding female appearance and its role in the academic/ professional setting. However, being a a first year graduate student, I would greatly appreciate people telling me whether what I’m wearing is appropriate for the task at hand. Now, before someone screams ‘slut shaming’: believe me, I know the difference. I just think that there is a right way to comment and there is a wrong way. Instead of forbidding male academics from commenting or giving helpful suggestions, I think it is more important to indicate what type of comments are inappropriate. Everyone knows that commenting on someone’s ass is a no-no, but what about advice? Personally, I believe defining an appropriate and inappropriate form of behavior is more effective than asking someone to stop the behavior entirely. These are some examples of the different forms that I can think of:

Inappropriate: This is a personal experience. During TA orientation, a woman on the panel directed the following comment at the female students.

Girls, please wear bras while teaching. You shouldn’t go around tantalizing your students in class.

This is more like slut-shaming to me. It implies it is the women’s fault if her students are too busy staring at her chest to learn.

Appropriate: These would be non gender-specific comments regarding appearance or clothing:

Hey, next time don’t wear sweatpants while teaching, it is unprofessional.

This comment can be directed at anyone irrespective of gender, sex, etc. And for people like me who love sweatpants, it can be pretty useful.

5. Make sure your department seminars, conference symposia, search committees, and panel discussions have a good gender balance

A general critique of this idea is that the seminars/ symposia/ panels should or will represent the distribution of the field. I wholeheartedly disagree with that critique simply because it fosters the idea that we shouldn’t attempt to alter the status quo.  Furthermore, the diversity in faculty or PIs does not necessarily represent the diversity of the student population. If so, they will not be capable of addressing the issues or representing the values of the academic community in a holistic manner.

6 & 7. Pay attention to who organizes the celebrations, gift-giving, or holiday gatherings. Volunteer when someone asks for a note-taker, coffee-run gopher, or lunch order-taker at your next meeting. 

The responsibility of organizer, coffee maker, cleaner, etc. most often falls onto women because as the article states we are ‘socially conditioned’ to volunteer for these tasks. Not to say that we always do it out of obligation, I personally love making coffee every morning. However, if no one else volunteers a woman is more likely to end up doing said task. On this point, I’ve heard people say – if you are aware of this then why don’t you stop volunteering? This isn’t the 1920s! That is a very privileged standpoint in my opinion. We don’t all come from the same background. I grew up in India where often women are expected to help in the kitchen, clean up, serve food at family gatherings. While I had the privilege of growing up in an extremely liberal and equal household, I was exposed to this through a variety of other social interactions. Till this date I feel compelled to set up, serve at and clean up after any event that I’m a part of – whether I’m an organizer or a guest. Some of us are conditioned to behave this way, and without male volunteers will probably end up doing this on every occasion.

10. During a talk Q&A session, call on women. Be a good moderator, and make sure men aren’t talking over women.

The criticism of this point is similar to one above: why don’t the women volunteer? My response is the same as well. While some of us are lucky enough to have been encouraged to think and share our ideas publicly, not everyone has. I have met enough women whose self esteem has been beaten down throughout their lives – literally and figuratively. Recovering from that takes time and help, especially with respect to sharing in a public setting. Considering intersectional identity is extremely important when criticizing this idea: not all women experience the same form of discrimination. There are more factors to consider here, and it will good to do so.

20. Finally, if you do all of the above, don’t expect a cookie. Your efforts may go unacknowledged or even unrecognized much of the time. Keep at it anyway, because you’re not out to get special recognition. You’re doing it because it’s the decent thing to do.

I know that congratulating someone every time they promote equality is not feasible. And I understand that if you make a big show about this behaviour it will come across as doing something extra, making discrimination the passable norm. However, people learn from positive reinforcement, even really really smart people. So, if you commend a colleague for making an effort to promote equality and diversity in something they did, they’re more likely to do it again. 

Preview image: http://www.usfca.edu/uploadedImages/News/Magazine/Fall_2009/images/science_people.gif

“Selection pressures” are metaphors. So are the “laws of physics.”

Coyne: Selection Pressure are metaphors

Why Evolution Is True

I mentioned offhand the other day that the notion of “selection pressures” in evolutionary biology is a metaphor, not dissimilar to the metaphor of a “selfish gene,” but Matthew convinced me that this idea was more profound than I thought (LOL!), so I’ll write a bit more about it.

A quick refresher: the other day Andrew Brown wrote one of his usual muddled columns in the Guardian, claiming, as he often does, that Richard Dawkins is a malign influence on evolutionary biology.  His argument was the usual blather that gene aren’t really “selfish,” and that this metaphor has led to deep confusion.  In the comments after his piece, Brown repeats this claim in response to a criticism (h/t to moleatthecounter for finding this):

Picture 1If you can’t read the above because the print’s too small, Brown says that “. . . Dawkins got confused by his own title. This confusion…

View original post 1,053 more words

Stewart Meets Dawkins – A Disappointment

I must start this post by saying, I love Jon Stewart; I think he is the funniest and one of the most influential people alive today. Also, he is a most often right about things. So, when I heard that Richard Dawkins was going to be on the daily show last night I was thrilled! Two of my favorite thinkers engaging in humorous discourse – what more could I ask for?  As it turns out, I could ask for a lot more.

The first question they tackled was whether the end of civilization will be brought about by religion strife or scientific advancement. First, I have issues with this question – and Dawkins addresses this – religion often uses scientific advances to bring down society. Scientists and engineers made bombs, but it is the religious fundamentalists who feel the need to use them. Stewart goes on to say that this ‘lets science off the hook’ and they may ultimately create something that results in worldwide disaster. I personally think that the goal of scientific research has never been to hurt or destroy but rather to create and understand. The creation of awful weapons has most often been asked of rather than offered up by scientists.

Stewart then goes on to paint a picture of irresponsible scientists and their creations destroying the world. As a side note: he fails to acknowledge the difference between scientists and engineers.  Stewart evidently isn’t aware of all the regulatory, ethics and permitting committees that do such a great job of maintaining the hoops that many of us have to jump through to get things done. There may have been a time for irresponsible science, but it isn’t now; if anything, the community learns from previous mistakes and becomes more responsible every year. Finally, it isn’t the questions that do harm but the use of the answers. You shouldn’t attempt to curb the curiosity, but you should regulate the applications.

Dawkins on The Daily Show (9/24/2013)

In the second part of the interview the conversation moves away from the fear of scientific advancement and back to religion. Stewart attempts to place religion with positive cultural products such as poetry and music. The biggest problem with this idea is that religion requires blind faith in ideas that are highly improbably and poetry does not. Truth to a religious person is what they make it or what they are told rather than fact. This is inherently dangerous. At this point Stewart veers dangerously close to the ‘since the scientists don’t know exactly what happens therefore religion’ argument used most famously by Ray Comfort. Believe me, it hurts me to compare the two. Stewart asks Dawkins whether he knows what happens to us after we die and then jumps on him when he doesn’t know for sure. He proceeds to use the there is a possibility that something happens to our consciousness after death bait. No scientist can resist this bait, simply because we will admit that anything is possible, however improbable. Just because something is possible, that doesn’t mean it is true.

At the end of the second segment, the conversation circles back to the idea the religion is a human construct and therefore our brains are flawed. I do support the idea that our brains are flawed, but Stewart goes on to say since science comes from our brains it must be flawed too. I agree with this as well, science makes mistakes. However, the trend of science is to improve and surpass what has come before us. We used to believe the universe was constant, the earth was flat, and species were unchanging: those were all mistakes. When the scientific communities realized these were mistakes they were rectified and ideas changed.  To address the threat of scientific advancement idea: science and engineering advancements led to flux of fossil fuels into the atmosphere resulting in global warming. Scientists discovered that this was an issue and have united in challenging our dirty energy lifestyles and have investigated and developed alternatives. In all the cases mentioned above it has been the religious who have remained staunch in their beliefs and refused to yield to new evidence. This is what separates religion from science, despite their shared usage of the human brain. I thought Jon Stewart knew that.

You can watch the interview here and be disappointed for yourself>>> Extended interview