From 0b4f825e0736e9cb0aed0f79b9c03bc18444cfb0 Mon Sep 17 00:00:00 2001 From: Sherine Awad Date: Wed, 7 Jan 2015 14:22:02 -0500 Subject: [PATCH 1/6] remove addendum lines in 5-mapping --- metagenomics/5-mapping-and-quantitation.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/metagenomics/5-mapping-and-quantitation.txt b/metagenomics/5-mapping-and-quantitation.txt index 30935c6..76502c9 100644 --- a/metagenomics/5-mapping-and-quantitation.txt +++ b/metagenomics/5-mapping-and-quantitation.txt @@ -1,7 +1,6 @@ ====================================== 5. Mapping and abundance quantitation ====================================== ->>>>>>> a34a904a7a0173ddffd4e6aff6e57547749cbd31 .. shell start From 89419896a72a19e4fdf6222bd959da6f32dea6d4 Mon Sep 17 00:00:00 2001 From: Sherine Awad Date: Fri, 27 Feb 2015 16:38:34 -0500 Subject: [PATCH 2/6] update index.txt --- metagenomics/index.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/metagenomics/index.txt b/metagenomics/index.txt index f85546c..dff5c1c 100644 --- a/metagenomics/index.txt +++ b/metagenomics/index.txt @@ -20,7 +20,8 @@ for the latest released version. 4-assemble 5-mapping-and-quantitation 6-annotating - installing-blastkit + 7-quast-evaluation + 8-installing-blastkit Reference material ------------------ From d546acbef3f91e4db67f45b8cfbf2a33220de240 Mon Sep 17 00:00:00 2001 From: Sherine Awad Date: Fri, 27 Feb 2015 16:41:09 -0500 Subject: [PATCH 3/6] Update index.txt --- metagenomics/8-installing-blastkit.txt | 106 +++++++++++++++++++++++++ 1 file changed, 106 insertions(+) create mode 100644 metagenomics/8-installing-blastkit.txt diff --git a/metagenomics/8-installing-blastkit.txt b/metagenomics/8-installing-blastkit.txt new file mode 100644 index 0000000..c7f4de0 --- /dev/null +++ b/metagenomics/8-installing-blastkit.txt @@ -0,0 +1,106 @@ +=============================== +7. BLASTing your assembled data +=============================== + +One thing everyone wants to do is BLAST sequence data, right? Here's a +simple way to set up a stylish little BLAST server that lets you search +your newly assembled sequences. + +Installing blastkit +------------------- + +Installing some prerequisites:: + + pip install pygr + pip install whoosh + pip install git+https://github.com/ctb/pygr-draw.git + pip install git+https://github.com/ged-lab/screed.git + apt-get -y install lighttpd + +and configure them:: + + cd /etc/lighttpd/conf-enabled + ln -fs ../conf-available/10-cgi.conf ./ + echo 'cgi.assign = ( ".cgi" => "" )' >> 10-cgi.conf + echo 'index-file.names += ( "index.cgi" ) ' >> 10-cgi.conf + + /etc/init.d/lighttpd restart + +Next, install BLAST:: + + cd /root + + curl -O ftp://ftp.ncbi.nih.gov/blast/executables/release/2.2.24/blast-2.2.24-x64-linux.tar.gz + tar xzf blast-2.2.24-x64-linux.tar.gz + cp blast-2.2.24/bin/* /usr/local/bin + cp -r blast-2.2.24/data /usr/local/blast-data + +And put in blastkit:: + + cd /root + git clone https://github.com/ctb/blastkit.git -b ec2 + cd blastkit/www + ln -fs $PWD /var/www/blastkit + + mkdir files + chmod a+rxwt files + chmod +x /root + +and run check.py:: + + cd /root/blastkit + python ./check.py + +It should say everything is OK. + +Adding the data +--------------- + +If you've just finished annotating a metagenome assembly +(:doc:`6-annotating`) then +you can do this to copy your newly generated assembly into the right place:: + + cp /mnt/work/metag/testasm.faa /root/blastkit/db/db-prot.fa + +Alternatively, you can grab our version of the assembly (from running this +tutorial):: + + cd /root/blastkit + curl -O http://athyra.idyll.org/~t/testasm.faa + mv testasm.faa db/db-prot.fa + +Formatting the database +~~~~~~~~~~~~~~~~~~~~~~~ + +After you've done either of the above, format and install the database +for blastkit:: + + cd /root/blastkit + formatdb -i db/db-prot.fa -o T -p T + python index-db.py db/db-prot.fa + +Done! + +.. note:: + + You can install any file of protein sequences you want this way; just copy + it into /root/blastkit/db/db-prot.fa and run the indexing commands, above. + +Running blastkit +---------------- + +Figure out what your machine name is +(ec2-???-???-???-???.compute-1.amazonaws.com) and go to:: + + http://machine-name/blastkit/ + +Make sure you have enabled port 80 in your security settings on Amazon. + +(If you're using the human data set, try this sequence:: + + MYLYTSYGTYQFLNQIKLNHQERNLFQFSTNDSSIILEESEGKSILKHPSSYQVIDSTGE + FNEHHFYSAIFVPTSEDHRQQLEKKLLHVDVPLSNFGGFKSYRLLKPTEGSTYKIYFGFA + NRTAYEDFKASDIFNENFSKDALSQYFGASGQHSSYFERYLYPIEDH + + +It should match something in your assembly.) From 15edfd7c0cf9903496bb8bca23f79f9de4c27926 Mon Sep 17 00:00:00 2001 From: Sherine Awad Date: Tue, 3 Mar 2015 11:37:15 -0500 Subject: [PATCH 4/6] fix conflicts --- metagenomics/5-mapping-and-quantitation.txt | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/metagenomics/5-mapping-and-quantitation.txt b/metagenomics/5-mapping-and-quantitation.txt index 6f402f2..90a25e6 100644 --- a/metagenomics/5-mapping-and-quantitation.txt +++ b/metagenomics/5-mapping-and-quantitation.txt @@ -1,13 +1,6 @@ -===================================== -5. Mapping and abundance quantitation -===================================== -======= -======= ====================================== -6. Mapping and abundance quantitation +5. Mapping and abundance quantitation ====================================== -======= -======= .. shell start From e809e7dc1ae8c7d32588dd9f75c8a2cffa13daaf Mon Sep 17 00:00:00 2001 From: Sherine Awad Date: Tue, 3 Mar 2015 11:42:26 -0500 Subject: [PATCH 5/6] remove redundant file in the directory --- metagenomics/newfile | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 metagenomics/newfile diff --git a/metagenomics/newfile b/metagenomics/newfile deleted file mode 100644 index e69de29..0000000 From 7c3cc7b0e1c65cd909b146400b4a56412871d6be Mon Sep 17 00:00:00 2001 From: Sherine Awad Date: Tue, 3 Mar 2015 11:50:32 -0500 Subject: [PATCH 6/6] remove redundant line --- metagenomics/6-annotating.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/metagenomics/6-annotating.txt b/metagenomics/6-annotating.txt index 7cf9883..39b11a8 100644 --- a/metagenomics/6-annotating.txt +++ b/metagenomics/6-annotating.txt @@ -5,7 +5,6 @@ .. :: - Installing Prokka =================