scGPT环境配置过程

.markdown-body { line-height: 1.75; font-weight: 400; font-size: 16px; overflow-x: hidden; color: rgba(37, 41, 51, 1) }
.markdown-body h1, .markdown-body h2, .markdown-body h3, .markdown-body h4, .markdown-body h5, .markdown-body h6 { line-height: 1.5; margin-top: 35px; margin-bottom: 10px; padding-bottom: 5px }
.markdown-body h1 { font-size: 24px; line-height: 38px; margin-bottom: 5px }
.markdown-body h2 { font-size: 22px; line-height: 34px; padding-bottom: 12px; border-bottom: 1px solid rgba(236, 236, 236, 1) }
.markdown-body h3 { font-size: 20px; line-height: 28px }
.markdown-body h4 { font-size: 18px; line-height: 26px }
.markdown-body h5 { font-size: 17px; line-height: 24px }
.markdown-body h6 { font-size: 16px; line-height: 24px }
.markdown-body p { line-height: inherit; margin-top: 22px; margin-bottom: 22px }
.markdown-body img { max-width: 100% }
.markdown-body hr { border-top: 1px solid rgba(221, 221, 221, 1); border-right: none; border-bottom: none; border-left: none; margin-top: 32px; margin-bottom: 32px }
.markdown-body code { border-radius: 2px; overflow-x: auto; background-color: rgba(255, 245, 245, 1); color: rgba(255, 80, 44, 1); font-size: 0.87em; padding: 0.065em 0.4em }
.markdown-body code, .markdown-body pre { font-family: Menlo, Monaco, Consolas, Courier New, monospace }
.markdown-body pre { overflow: auto; position: relative; line-height: 1.75 }
.markdown-body pre>code { font-size: 12px; padding: 15px 12px; margin: 0; word-break: normal; display: block; overflow-x: auto; color: rgba(51, 51, 51, 1); background: rgba(248, 248, 248, 1) }
.markdown-body a { text-decoration: none; color: rgba(2, 105, 200, 1); border-bottom: 1px solid rgba(209, 233, 255, 1) }
.markdown-body a:active, .markdown-body a:hover { color: rgba(39, 91, 140, 1) }
.markdown-body table { display: inline-block !important; font-size: 12px; width: auto; max-width: 100%; overflow: auto; border: 1px solid rgba(246, 246, 246, 1) }
.markdown-body thead { background: rgba(246, 246, 246, 1); color: rgba(0, 0, 0, 1); text-align: left }
.markdown-body tr:nth-child(2n) { background-color: rgba(252, 252, 252, 1) }
.markdown-body td, .markdown-body th { padding: 12px 7px; line-height: 24px }
.markdown-body td { min-width: 120px }
.markdown-body blockquote { color: rgba(102, 102, 102, 1); padding: 1px 23px; margin: 22px 0; border-left: 4px solid rgba(203, 203, 203, 1); background-color: rgba(248, 248, 248, 1) }
.markdown-body blockquote:after { display: block; content: "" }
.markdown-body blockquote>p { margin: 10px 0 }
.markdown-body ol, .markdown-body ul { padding-left: 28px }
.markdown-body ol li, .markdown-body ul li { margin-bottom: 0; list-style: inherit }
.markdown-body ol li .task-list-item, .markdown-body ul li .task-list-item { list-style: none }
.markdown-body ol li .task-list-item ol, .markdown-body ol li .task-list-item ul, .markdown-body ul li .task-list-item ol, .markdown-body ul li .task-list-item ul { margin-top: 0 }
.markdown-body ol ol, .markdown-body ol ul, .markdown-body ul ol, .markdown-body ul ul { margin-top: 3px }
.markdown-body ol li { padding-left: 6px }
.markdown-body .contains-task-list { padding-left: 0 }
.markdown-body .task-list-item { list-style: none }
@media (max-width: 720px) { .markdown-body h1 { font-size: 24px } .markdown-body h2 { font-size: 20px } .markdown-body h3 { font-size: 18px } }.markdown-body pre, .markdown-body pre>code.hljs { color: rgba(51, 51, 51, 1); background: rgba(248, 248, 248, 1) }
.hljs-comment, .hljs-quote { color: rgba(153, 153, 136, 1); font-style: italic }
.hljs-keyword, .hljs-selector-tag, .hljs-subst { color: rgba(51, 51, 51, 1); font-weight: 700 }
.hljs-literal, .hljs-number, .hljs-tag .hljs-attr, .hljs-template-variable, .hljs-variable { color: rgba(0, 128, 128, 1) }
.hljs-doctag, .hljs-string { color: rgba(221, 17, 68, 1) }
.hljs-section, .hljs-selector-id, .hljs-title { color: rgba(153, 0, 0, 1); font-weight: 700 }
.hljs-subst { font-weight: 400 }
.hljs-class .hljs-title, .hljs-type { color: rgba(68, 85, 136, 1); font-weight: 700 }
.hljs-attribute, .hljs-name, .hljs-tag { color: rgba(0, 0, 128, 1); font-weight: 400 }
.hljs-link, .hljs-regexp { color: rgba(0, 153, 38, 1) }
.hljs-bullet, .hljs-symbol { color: rgba(153, 0, 115, 1) }
.hljs-built_in, .hljs-builtin-name { color: rgba(0, 134, 179, 1) }
.hljs-meta { color: rgba(153, 153, 153, 1); font-weight: 700 }
.hljs-deletion { background: rgba(255, 221, 221, 1) }
.hljs-addition { background: rgba(221, 255, 221, 1) }
.hljs-emphasis { font-style: italic }
.hljs-strong { font-weight: 700 }

第一步：安装创建一个新的环境

conda create -n scgpt

第二步:进入scgpt环境 安装python、r-base、r-devtools

conda activate scgpt

conda install python=3.7.14 r-base=3.6.1 r-devtools

第三步：使用pip安装flash-attn（版本1.0.5）和orbax(版本0.1.0)，以及wandb

pip install flash-attn==1.0.5

pip install orbax==0.1.0

pip install wandb

第四步：使用pip安装scGPT的其他包

pip install scgpt

安装数据下载的包：cellxgene-census(1.2.1版本适合python3.7版本，1.2.1以上版本适合python3.8)

pip install cellxgene-census==1.2.1

完