Changes between Version 8 and Version 9 of FAQ

Timestamp:

09/02/21 14:15:50 (3 years ago)

Author:

gbell

Comment:

--

FAQ

@@ -37 +37 @@
 1. Why do I get '''[#wi_ncbi_blast different BLAST results]'''  from [[http://tak.wi.mit.edu/blast/ | WI]] and NCBI Blast? [[br]] [[br]]
 1. How do I run '''[#tophat_bowtie tophat/bowtie on the LSF with a gzip'd tar (*.tar.gz)]''' file?  [[br]] [[br]]
-
+1. How can I run '''[#alphafold AlphaFold 2.0]''' here at Whitehead?  [[br]] [[br]]
 ----
 Answers to Frequently Asked Questions
@@ -208 +208 @@
   * bsub bash -c "tophat ... <(tar xvzfO ...) <(tar xvzfO ...)", this is using process substitution 
     * eg. bsub bash -c "tophat -p 10 -g 1 -o mapped_data_SRR905147_unique -N 2 -I 10000 --segment-length 25 --segment-mismatches 2 hg19 <(tar xvzfO s_2_1_sequence.txt.tar.gz ACTTGA-s_2_1_sequence.txt) <(tar xvzfO CAGATC-s_2_1_sequence.txt.tar.gz CAGATC-s_2_1_sequence.txt)"
+1. [=#alphafold How can I run '''AlphaFold 2.0''' here at Whitehead?]
+  * Log on to tempest.wi.mit.edu -- ask IT if your account doesn't allow you to do this.
+    * ssh -Y USERNAME@tempest
+  * Modify the environment with a path to the required data:
+    * export ALPHAFOLD_DATA_PATH=/alphafold/data
+  * Run the main AlphaFold 2.0 command, like
+   {{{
+singularity run -B $ALPHAFOLD_DATA_PATH:/data -B .:/etc \
+--pwd /app/alphafold \
+--nv /alphafold/alphafold_2.0.0.sif \
+--fasta_paths=/data/query.fasta \
+--output_dir=/tmp/AlphaFold_output \
+--model_names=model_1 \
+--preset=full_dbs \
+--data_dir=/data \
+--max_template_date=2020-05-14 \
+--uniref90_database_path=/data/uniref90/uniref90.fasta \
+--mgnify_database_path=/data/mgnify/mgy_clusters.fa \
+--uniclust30_database_path=/data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
+--bfd_database_path=/data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
+--pdb70_database_path=/data/pdb70/pdb70 \
+--template_mmcif_dir=/data/pdb_mmcif/mmcif_files \
+--obsolete_pdbs_path=/data/pdb_mmcif/obsolete.dat
+}}}
+  * More information, including an explanation of the output files, is here: https://github.com/deepmind/alphafold