diff --git a/blast/README.md b/blast/README.md index c752f56..191453b 100644 --- a/blast/README.md +++ b/blast/README.md @@ -15,7 +15,7 @@ cd ./makeflow-examples/blast First, obtain a blast binary suitable for your architecture. (about 30MB) ``` -wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz +wget https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz tar xvzf blast-2.2.26-x64-linux.tar.gz ``` @@ -24,9 +24,9 @@ Next, copy the main executable into the working directory. cp blast-2.2.26/bin/blastall . ``` -Obtain a nucleotide database suitable for searching. (about 400MB) +Obtain a nucleotide database suitable for searching. (about 1.5GB) ``` -wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.44.tar.gz +wget https://ftp.ncbi.nlm.nih.gov/blast/db/nt.044.tar.gz mkdir nt tar -C nt -xvzf nt.44.tar.gz ``` @@ -42,8 +42,8 @@ If everything is working correctly, you should see output that starts like this: ``` BLASTN 2.2.26 [Sep-21-2011] -Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, -Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), +Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, +Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. @@ -94,7 +94,7 @@ makeflow --jx blast.jx makeflow --json blast.json ``` -The number and length of sequences can be adjusted for your needs, with the first number +The number and length of sequences can be adjusted for your needs, with the first number adjusting the number of contigs and the second adjusting the length of these contigs. `fasta_generator` produces contigs containing random AGCT sequences. diff --git a/blast/makeflow_blast b/blast/makeflow_blast index bf3cb75..7fd5647 100755 --- a/blast/makeflow_blast +++ b/blast/makeflow_blast @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python2 # CCTOOLS_PYTHON_VERSION 2.7 2.6 # Copyright (C) 2011- The University of Notre Dame diff --git a/bwa/make_bwa_workflow b/bwa/make_bwa_workflow index dcc9d26..50f750b 100755 --- a/bwa/make_bwa_workflow +++ b/bwa/make_bwa_workflow @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python2 # CCTOOLS_PYTHON_VERSION 2.7 2.6 # #Copyright (C) 2013- The University of Notre Dame diff --git a/ssaha/README.md b/ssaha/README.md index d30ad2b..6075ec8 100755 --- a/ssaha/README.md +++ b/ssaha/README.md @@ -4,7 +4,7 @@ SSAHA Workflow Example ---------------------- This example workflow demonstrates how to parallelize the -SSAHA2 (Sequence Search and Alignment by Hasing Algorithm) +SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) tool published by the Sanger institute. If you have not done so already, please clone this example repository like so: @@ -17,7 +17,7 @@ First, download and install a suitable binary for SSAHA2: ``` export SSAHA_BINARY=ssaha2_v2.5.5_x86_64 -wget ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/${SSAHA_BINARY}.tgz +wget https://ftp.sanger.ac.uk/pub/resources/software/ssaha2/${SSAHA_BINARY}.tgz tar xvzf ${SSAHA_BINARY}.tgz cp ${SSAHA_BINARY}/ssaha2 . ```